Combination therapy for treating cancer

ABSTRACT

The present disclosure relates to compositions comprising inhibitors of human histone methyltransferase EZH2 and one or more other therapeutic agents (such as tyrosine kinase inhibitors or VEGF/VEGFR inhibitors), particularly anticancer agents such as sunitinib, and methods of combination therapy for administering to subjects in need thereof for the treatment of cancer.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 15/567,838, filed Oct. 19, 2017 (now U.S. Pat. No. 10,456,407), which is a U.S. National Phase application, filed under 35 U.S.C. § 371, of International Application No. PCT/US2016/028425, filed Apr. 20, 2016, which claims priority to, and the benefit of, U.S. Provisional Application No. 62/150,185, filed Apr. 20, 2015, the entire contents of each of which are incorporated herein by reference in their entireties.

INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING

The contents of the text file named “EPIZ048N01USSequenceListing.txt”, which was created on Mar. 29, 2018, and is 46,146 bytes in size, are incorporated herein by reference in their entireties.

FIELD OF THE DISCLOSURE

This disclosure relates to compositions comprising inhibitors of human histone methyltransferase EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono- through tri-methylation of lysine 27 on histone H3 (H3-K27), and one or more other therapeutic agents, particularly anticancer agents, and methods of combination therapy for treating cancer.

BACKGROUND

Combination-therapy treatments for cancer have become more common, in part due to the perceived advantage of attacking the disease via multiple avenues. Although many effective combination-therapy treatments have been identified over the past few decades; in view of the continuing high number of deaths each year resulting from cancer, a continuing need exists to identify effective therapeutic regimens for use in anticancer treatment.

SUMMARY

The instant disclosure is based partially upon the discovery that EZH2 inhibition increases sensitivity to anti-VEGF agent such as sunitinib. Accordingly, one aspect of this disclosure relates to a method for treating cancer in a subject (e.g., a patient) in need thereof, by administering a therapeutically effective amount of an EZH2 inhibitor and one or more tyrosine kinase inhibitors or VEGF/VEGFR inhibitors. For example, the cancer is resistant to tyrosine kinase inhibitor treatment or resistant to VEGF/VEGFR inhibitor treatment. For example, the cancer is renal cell carcinoma (e.g., advanced clear cell renal cell carcinoma).

The instant disclosure is based partially upon the discovery that EZH2 inhibitors, such as Compound 44 and glucocorticoid receptor agonists (GRags), such as Prednisone, Prednisolone or Dexamethasone, cooperate to dramatically enhance therapeutic activity in cancer. The combination of Compound 44 and prednisolone extends the range of cells that are sensitive to EZH2 inhibition, from mutant-bearing only to all GCB NHL cells.

The present disclosure directs to methods for treating cancer in a patient in need thereof by administering a therapeutically effective amount of an EZH2 inhibitor and one or more therapeutic agents selected from the group consisting of a glucocorticoid receptor agonist (GRag), CHOP and a BCL2 inhibitor. For example, the BCL2 inhibitor is navitoclax.

In some embodiments, the cancer is NHL of the germinal center B subtype.

In some embodiments, the cancer is an EZH2 mutant cancer. Alternatively, the cancer is an EZH2 wild type cancer.

In some embodiments, the cancer is an EZH2 inhibitor resistant or refractory cancer.

The EZH2 inhibitor and the GRag may be administered simultaneously or sequentially. For example, the EZH2 inhibitor is administered prior to administration of the GRag.

In one aspect of the disclosure, the combination therapies described here induce a modulation in the expression of specific genes, for example, glucocorticoid target genes. As used herein, glucocorticoid target genes refer to genes that are directly or indirectly regulated by glucocorticoid. In certain embodiments a gene is upregulated following the combination therapies described herein. In certain embodiments the gene is Sestrin, TNF and/or GILZ. In certain embodiments these genes can be used as biomarkers, i.e., the gene expression profile can be used to identify patients suitable for the combination therapies described herein. In certain embodiments, the gene expression can be used to monitor or evaluate the dosage or efficacy of the combination therapies described herein.

In one embodiment the cancer is a hematological cancer. In a certain embodiment the cancer is a lymphoma. In a certain embodiment the cancer is a Non-Hodgkin's Lymphoma (NHL) or Diffuse Large B-cell Lymphoma (DLBCL) of the germinal center B subtype (GCB).

In one embodiment the therapeutic activity of the EZH2 inhibitor is enhanced by the GRag in EZH2 mutant bearing cells.

In one aspect of the disclosure, the EZH2 inhibitors enhance the GRag therapeutic activity in WT EZH2 cells. In one embodiment, the cells are WT GCB EZH2 cells. In a certain embodiment of the disclosure, the EZH2 inhibitor is Compound 44 and the GRag is Prednisone.

One aspect of the disclosure is based upon the discovery that the combination of the EZH2 inhibitor and the GRag reverses the insensitivity in EZH2-inhibitor resistant or refractory mutant cells, including EZH2 mutation bearing cells.

In mutant EZH2 GCB lymphoma cells, combination benefit was also observed with all the single components of the CHOP chemotherapy regime. In addition, in two different EZH2 mutant xenograft models, strong combination benefit with CHOP, and this effect was preserved in a study in a third EZH2 mutant xenograft model in which doxorubicin was omitted from the chemotherapy regime.

The present disclosure is based upon the discovery that EZH2 histone methyltransferase inhibitors and other anti-cancer agents can be used in combination to treat certain tumors with superior results than those achieved by treating tumors with EZH2 histone methyltransferase inhibitors and the anti-cancer agents alone. Accordingly, the present disclosure provides a composition comprising an EZH2 histone methyltransferase inhibitor and one or more other therapeutic agents, and methods for their use to treat diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, e.g., cancer. In a certain embodiment, the present disclosure features a composition comprising Compound 44 and prednisone. In certain embodiments, the present disclosure features a combination therapy comprising Compound 44 and navitoclax. The present disclosure also includes methods for combination therapies comprising EZH2 histone methyltransferase inhibitor and one or more therapeutic agents, such as a Compound 44 and prednisone, to treat cancer, e.g., GCB lymphoma, follicular lymphoma (FL) and diffuse cell large B-cell lymphoma (DCLBL). Specifically, the methods of the present disclosure are useful for treating or preventing cancer or inhibiting cancer cell proliferation.

In one aspect, the present disclosure features a composition comprising a compound of Formula (VIa) below and one or more other therapeutic agents (such as tyrosine kinase inhibitors) or a pharmaceutically acceptable salt or ester thereof.

The compounds of Formula (VIa) can include one or more of the following features:

Each of R_(a) and R_(b), independently is H or C₁-C₆ alkyl.

R_(a) and R_(b), together with the N atom to which they are attached, is a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, the C₁-C₆ alkyl and the 4 to 12-membered (e.g., 4 to 7-membered) heterocycloalkyl ring being optionally substituted with one or more -Q₃-T₃.

Q₃ is a bond or unsubstituted or substituted C₁-C₃ alkyl linker.

T₃ is H, halo, 4 to 7-membered heterocycloalkyl, C₁-C₃ alkyl, OR_(d), COOR_(d), —S(O)₂R_(d), or —NR_(d)R_(e), each of R_(d) and R_(e) independently being H or C₁-C₆ alkyl.

R₇ is C₁-C₆ alkyl, C₃-C₅ cycloalkyl or 4 to 12-membered (e.g., 4 to 7-membered) heterocycloalkyl, each optionally substituted with one or more -Q₅-T₅. For example, R₇ is not H.

R₇ is 4 to 7-membered heterocycloalkyl optionally substituted with one or more -Q₅-T₅.

R₇ is piperidinyl, tetrahydropyran, cyclopentyl, or cyclohexyl, each optionally substituted with one -Q₅-T₅.

T₅ is H, halo, C₁-C₆ alkyl, C₁-C₆ alkoxyl, C₃-C₅ cycloalkyl, C₆-C₁₀ aryl, or 4 to 12-membered (e.g., 4 to 7-membered) heterocycloalkyl.

Q₅ is a bond and T₅ is C₁-C₆ alkyl, C₃-C₅ cycloalkyl, or 4 to 12-membered (e.g., 4 to 7-membered) heterocycloalkyl.

Q₅ is CO, S(O)₂, or NHC(O); and T₅ is C₁-C₆ alkyl, C₁-C₆ alkoxyl, C₃-C₅ cycloalkyl, or 4 to 12-membered (e.g., 4 to 7-membered) heterocycloalkyl.

Q₅ is C₁-C₃ alkyl linker and T₅ is H or C₆-C₁₀ aryl.

Q₅ is C₁-C₃ alkyl linker and T₅ is C₃-C₅ cycloalkyl, 4 to 7-membered heterocycloalkyl, or S(O)_(q)R_(q).

R₇ is cyclopentyl or cyclohexyl, each optionally substituted with one -Q₅-T₅.

Q₅ is NHC(O) and T₅ is C₁-C₆ alkyl or C₁-C₆ alkoxy.

R₇ is isopropyl.

Each of R₂ and R₄, independently is H or C₁-C₆ alkyl optionally substituted with amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, or C₆-C₁₀ aryl.

R₈ is H, methyl, or ethyl.

R₈ is methyl.

R₈ is ethyl.

R₈ is 4 to 7-heterocycloalkyl, e.g., tetrahydropyran.

The present disclosure features a composition comprising a compound selected from Table 1 or a pharmaceutically acceptable salt or ester thereof and one or more other therapeutic agents.

For example, the EZH2 inhibitor is Compound 44 (also known as EPZ-6438, E7438) having the following formula:

or a pharmaceutically acceptable salt or solvate thereof and one or more other therapeutic agents.

For example, the EZH2 inhibitor is Compound A having the following formula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvates thereof.

For example, the EZH2 inhibitor is Compound B (also known as EPZ011989) having the following formula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvates thereof.

For example, the EZH2 inhibitor is Compound C having the following formula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvates thereof.

For example, the EZH2 inhibitor is GSK-126 having the following formula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvates thereof.

In this and other aspects of the disclosure, in one embodiment the other therapeutic agents are anticancer agents.

In this and other aspects of the disclosure, in one embodiment the other therapeutic agents are tyrosine kinase inhibitors. For example, the EZH2 inhibitor and the one or more tyrosine kinase inhibitors are administered simultaneously or sequentially. For example, the EZH2 inhibitor is administered prior to administration of the one or more tyrosine kinase inhibitors.

In this and other aspects of the disclosure, in one embodiment the other therapeutic agents are or VEGF/VEGFR inhibitors. For example, the EZH2 inhibitor and the one or more VEGF/VEGFR inhibitors are administered simultaneously or sequentially. For example, the EZH2 inhibitor is administered prior to administration of the one or more VEGF/VEGFR inhibitors.

In this and other aspects of the disclosure, in one embodiment the other therapeutic agents are glucocorticoids.

In this and other aspects of the disclosure, in one embodiment the other therapeutic agents are selected from prednisone, prednisolone, cyclophosphamide, vincristine, doxorubicin, mafosfamide, cisplatin, AraC, everolimus, decitabine, dexamethasone, and analogs, derivatives, or combinations thereof.

In this and other aspects of the disclosure, in one embodiment the other therapeutic agent is prednisone, or an analog or derivative thereof.

The present disclosure also provides pharmaceutical compositions comprising a compound selected from those of Formulae (I)-(VIa) disclosed herein or pharmaceutical acceptable salts thereof and one or more therapeutic agents, and a pharmaceutically acceptable carrier.

The present disclosure also provides pharmaceutical compositions comprising a compound selected from Table I, one or more other therapeutic agents, or pharmaceutically acceptable salts thereof, and a pharmaceutically acceptable carrier.

The present disclosure also provides pharmaceutical compositions comprising a compound selected from those of Formulae (I)-(VIa) disclosed herein or pharmaceutically acceptable salts thereof, one or more other therapeutic agents, and a pharmaceutically acceptable carrier.

Another aspect of this disclosure is a method for treating or preventing a disease by administering to a subject in need thereof a therapeutically effective amount of a composition comprising a compound of Formulae (I)-(VIa), or a pharmaceutically acceptable salt thereof, and one or more additional therapeutic agents. The disease of the present disclosure can be influenced, treated, or prevented by modulating the methylation status of histones or other proteins. For example, the disease is cancer, a precancerous condition, or a neurological disease. Preferably, the lymphoma is non-Hodgkin lymphoma, follicular lymphoma or diffuse large B-cell lymphoma. Alternatively, the leukemia is chronic myelogenous leukemia (CML). The precancerous condition is, e.g., myelodysplastic syndromes (MDS, formerly known as preleukemia).

The subject of the present disclosure includes any human subject who has been diagnosed with, has symptoms of, or is at risk of developing a cancer or a precancerous condition. The subject of the present disclosure includes any human subject expressing a mutant EZH2. For example, a mutant EZH2 comprises one or more mutations, wherein the mutation is a substitution, a point mutation, a nonsense mutation, a missense mutation, a deletion, or an insertion. A mutant EZH2 of the present disclosure may comprise a mutation in the substrate pocket domain as defined in SEQ ID NO: 6. A mutant EZH2 may have a substitution at amino acid Y641. Preferably, the mutant EZH2 has one of the following mutations: substitution of phenylalanine (F) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641F); a substitution of histidine (H) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641H); a substitution of asparagine (N) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641N); a substitution of serine (S) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641S); and a substitution of cysteine (C) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641C).

Other mutations of EZH2 may include, but are not limited to: a substitution of glycine (G) for the wild type residue alanine (A) at amino acid position 677 of SEQ ID NO: 1 (A677G); a substitution of valine (V) for the wild type residue alanine (A) at amino acid position 687 of SEQ ID NO: 1 (A687V); a substitution of methionine (M) for the wild type residue valine (V) at amino acid position 674 of SEQ ID NO: 1 (V674M); a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 685 of SEQ ID NO: 1 (R685H); a substitution of cysteine (C) for the wild type residue arginine (R) at amino acid position 685 of SEQ ID NO: 1 (R685C); a substitution of serine (S) for the wild type residue asparagine (N) at amino acid position 322 of SEQ ID NO: 3 (N322S), a substitution of glutamine (Q) for the wild type residue arginine (R) at amino acid position 288 of SEQ ID NO: 3 (R288Q), a substitution of isoleucine (I) for the wild type residue threonine (T) at amino acid position 573 of SEQ ID NO: 3 (T5731), a substitution of glutamic acid (E) for the wild type residue aspartic acid (D) at amino acid position 664 of SEQ ID NO: 3 (D664E), a substitution of glutamine (Q) for the wild type residue arginine (R) at amino acid position 458 of SEQ ID NO: 5 (R458Q), a substitution of lysine (K) for the wild type residue glutamic acid (E) at amino acid position 249 of SEQ ID NO: 3 (E249K), a substitution of cysteine (C) for the wild type residue arginine (R) at amino acid position 684 of SEQ ID NO: 3 (R684C), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 628 of SEQ ID NO: 11 (R628H), a substitution of histidine (H) for the wild type residue glutamine (Q) at amino acid position 501 of SEQ ID NO: 5 (Q501H), a substitution of asparagine (N) for the wild type residue aspartic acid (D) at amino acid position 192 of SEQ ID NO: 3 (D192N), a substitution of valine (V) for the wild type residue aspartic acid (D) at amino acid position 664 of SEQ ID NO: 3 (D664V), a substitution of leucine (L) for the wild type residue valine (V) at amino acid position 704 of SEQ ID NO: 3 (V704L), a substitution of serine (S) for the wild type residue proline (P) at amino acid position 132 of SEQ ID NO: 3 (P132S), a substitution of lysine (K) for the wild type residue glutamic acid (E) at amino acid position 669 of SEQ ID NO: 11 (E669K), a substitution of threonine (T) for the wild type residue alanine (A) at amino acid position 255 of SEQ ID NO: 3 (A255T), a substitution of valine (V) for the wild type residue glutamic acid (E) at amino acid position 726 of SEQ ID NO: 3 (E726V), a substitution of tyrosine (Y) for the wild type residue cysteine (C) at amino acid position 571 of SEQ ID NO: 3 (C571Y), a substitution of cysteine (C) for the wild type residue phenylalanine (F) at amino acid position 145 of SEQ ID NO: 3 (F145C), a substitution of threonine (T) for the wild type residue asparagine (N) at amino acid position 693 of SEQ ID NO: 3 (N693T), a substitution of serine (S) for the wild type residue phenylalanine (F) at amino acid position 145 of SEQ ID NO: 3 (F145S), a substitution ofhistidine (H) for the wild type residue glutamine (Q) at amino acid position 109 of SEQ ID NO: 11 (Q109H), a substitution of cysteine (C) for the wild type residue phenylalanine (F) at amino acid position 622 of SEQ ID NO: 11 (F622C), a substitution of arginine (R) for the wild type residue glycine (G) at amino acid position 135 of SEQ ID NO: 3 (G135R), a substitution of glutamine (Q) for the wild type residue arginine (R) at amino acid position 168 of SEQ ID NO: 5 (R168Q), a substitution of arginine (R) for the wild type residue glycine (G) at amino acid position 159 of SEQ ID NO: 3 (G159R), a substitution of cysteine (C) for the wild type residue arginine (R) at amino acid position 310 of SEQ ID NO: 5 (R310C), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 561 of SEQ ID NO: 3 (R561H), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 634 of SEQ ID NO: 11 (R634H), a substitution of arginine (R) for the wild type residue glycine (G) at amino acid position 660 of SEQ ID NO: 3 (G660R), a substitution of cysteine (C) for the wild type residue tyrosine (Y) at amino acid position 181 of SEQ ID NO: 3 (Y181C), a substitution of arginine (R) for the wild type residue histidine (H) at amino acid position 297 of SEQ ID NO: 3 (H297R), a substitution of serine (S) for the wild type residue cysteine (C) at amino acid position 612 of SEQ ID NO: 11 (C612S), a substitution of tyrosine (Y) for the wild type residue histidine (H) at amino acid position 694 of SEQ ID NO: 3 (H694Y), a substitution of alanine (A) for the wild type residue aspartic acid (D) at amino acid position 664 of SEQ ID NO: 3 (D664A), a substitution of threonine (T) for the wild type residue isoleucine (I) at amino acid position 150 of SEQ ID NO: 3 (I150T), a substitution of arginine (R) for the wild type residue isoleucine (I) at amino acid position 264 of SEQ ID NO: 3 (1264R), a substitution of leucine (L) for the wild type residue proline (P) at amino acid position 636 of SEQ ID NO: 3 (P636L), a substitution of threonine (T) for the wild type residue isoleucine (I) at amino acid position 713 of SEQ ID NO: 3 (I713T), a substitution of proline (P) for the wild type residue glutamine (Q) at amino acid position 501 of SEQ ID NO: 5 (Q501P), a substitution of glutamine (Q) for the wild type residue lysine (K) at amino acid position 243 of SEQ ID NO: 3 (K243Q), a substitution of aspartic acid (D) for the wild type residue glutamic acid (E) at amino acid position 130 of SEQ ID NO: 5 (E130D), a substitution of glycine (G) for the wild type residue arginine (R) at amino acid position 509 of SEQ ID NO: 3 (R509G), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 566 of SEQ ID NO: 3 (R566H), a substitution of histidine (H) for the wild type residue aspartic acid (D) at amino acid position 677 of SEQ ID NO: 3 (D677H), a substitution of asparagine (N) for the wild type residue lysine (K) at amino acid position 466 of SEQ ID NO: 5 (K466N), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 78 of SEQ ID NO: 3 (R78H), a substitution of methionine (M) for the wild type residue lysine (K) at amino acid position 1 of SEQ ID NO: 6 (K6M), a substitution of leucine (L) for the wild type residue serine (S) at amino acid position 538 of SEQ ID NO: 3 (S538L), a substitution of glutamine (Q) for the wild type residue leucine (L) at amino acid position 149 of SEQ ID NO: 3 (L149Q), a substitution of valine (V) for the wild type residue leucine (L) at amino acid position 252 of SEQ ID NO: 3 (L252V), a substitution of valine (V) for the wild type residue leucine (L) at amino acid position 674 of SEQ ID NO: 3 (L674V), a substitution of valine (V) for the wild type residue alanine (A) at amino acid position 656 of SEQ ID NO: 3 (A656V), a substitution of aspartic acid (D) for the wild type residue alanine (A) at amino acid position 731 of SEQ ID NO: 3 (Y731D), a substitution of threonine (T) for the wild type residue alanine (A) at amino acid position 345 of SEQ ID NO: 3 (A345T), a substitution of aspartic acid (D) for the wild type residue alanine (A) at amino acid position 244 of SEQ ID NO: 3 (Y244D), a substitution of tryptophan (W) for the wild type residue cysteine (C) at amino acid position 576 of SEQ ID NO: 3 (C576W), a substitution of lysine (K) for the wild type residue asparagine (N) at amino acid position 640 of SEQ ID NO: 3 (N640K), a substitution of lysine (K) for the wild type residue asparagine (N) at amino acid position 675 of SEQ ID NO: 3 (N675K), a substitution of tyrosine (Y) for the wild type residue aspartic acid (D) at amino acid position 579 of SEQ ID NO: 11 (D579Y), a substitution of isoleucine (I) for the wild type residue asparagine (N) at amino acid position 693 of SEQ ID NO: 3 (N693I), and a substitution of lysine (K) for the wild type residue asparagine (N) at amino acid position 693 of SEQ ID NO: 3 (N693K).

Other mutations of EZH2 can include: a frameshift at amino acid position 730, 391, 461, 441, 235, 254, 564, 662, 715, 405, 685, 64, 73, 656, 718, 374, 592, 505, 730, or 363 of SEQ ID NO: 3, 5 or 11 or the corresponding nucleotide positions encoding the amino acid sequences mentioned above; a deletion of glutamic acid (E) and leucine (L) at amino acid positions 148 and 149 of SEQ ID NO: 3, 5 or 11, or a nonsense mutation at amino acid position 733, 25, 317, 62, 553, 328, 58, 207, 123, 63, 137, or 60 of SEQ ID NO: 3, 5 or 11.

A subject of the present disclosure may have resistance to any one or more other therapeutic agents or any of the compounds described herein. For example, the subject may have resistance to EZH inhibitors or prednisone.

The present disclosure features a method for inhibiting cancer cell proliferation comprising contacting said cancer cells with a composition comprising any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt thereof, and one or more additional therapeutic agent. Inhibiting cancer cell proliferation includes delaying cancer cell growth, inducing cell death, reducing cancer cell viability, inhibiting or delaying tumor growth, or reducing tumor size.

The present disclosure features methods of combination therapy wherein any compound of Formulae (I)-(VIa), or pharmaceutically acceptable salt thereof, and one or more other therapeutic agents are administered simultaneously or sequentially. For example, any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt thereof may be administered prior to administration of one or more other therapeutic agents. For example, any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt there or may be administered prior to administration of a composition comprising any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt thereof and one or more other therapeutic agents. Concurrent or sequential administration of any compound of Formulae (I)-(VIa) and/or each therapeutic agent can be effected by any appropriate route including, but not limited to, oral routes, intravenous routes, intramuscular routes, and direct absorption through mucous membrane tissues. The therapeutic agents can be administered by the same route or by different routes.

The methods of combination therapy featured in the present disclosure may result in a synergistic effect, wherein the effect of a combination of compounds or other therapeutic agents is greater than the sum of the effects resulting from administration of any of the compounds or other therapeutic agents as single agents. A synergistic effect may also be an effect that cannot be achieved by administration of any of the compounds or other therapeutic agents as single agents. The synergistic effect may include, but is not limited to, an effect of treating cancer by reducing tumor size, inhibiting tumor growth, or increasing survival of the subject. The synergistic effect may also include reducing cancer cell viability, inducing cancer cell death, and inhibiting or delaying cancer cell growth.

Compositions of the present disclosure can be administered at a dosage of 0.01 mg/kg per day to about 1000 mg/kg per day. Any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt thereof may be administered at a dosage of 0.01 mg/kg per day to about 1000 mg/kg per day. Any other therapeutic agent may be administered at a dosage of 0.01 mg/kg per day to about 1000 mg/kg per day.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In the specification, the singular forms also include the plural unless the context clearly dictates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents and other references mentioned herein are incorporated by reference. The references cited herein are not admitted to be prior art to the claimed invention. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods and examples are illustrative only and are not intended to be limiting.

Other features and advantages of the invention will be apparent from the following detailed description and claims.

BRIEF DESCRIPTIONS OF FIGURES

FIG. 1 is a scheme showing the design of in vitro combination assays.

Pre-treatment model A: Lymphoma cells were pretreated in flasks with 7 doses of Compound 44 (also called EZH-6438) or DMSO for 4 days. Cells were normalized and co-treated with Compound 44 and compound of interest (3 replicate plates in matrix of two compound combinations in a constant ratio) using the HP D300 digital dispenser. After 3 days of co-treatment, cell viability was measured via ATP content using CellTiter-Glo®. Pre-treatment models B and C: Lymphoma cells were pretreated with 1 dose of compound of interest or 7 doses of Compound 44 and DMSO for 4 days. Cells were then normalized and co-treated with 1 dose of compound of interest and 7 doses of Compound 44 and DMSO for 3 days. Viability was determined using Guava ViaCount® Reagent. Co-treatment Model: Lymphoma cells were treated with 7 doses of Compound 44 and 1 dose of compound of interest for either 4 or 7 days. Viability was determined using Guava ViaCount® Reagent.

FIG. 2 is a scheme showing the data analysis using Chou-Talalay method. Synergy quantification is performed using the Chou-Talalay method³ for drug combination. The Combination Index (CI) equation offers a quantitative definition for additivity (CI=1), synergism (CI<1), and antagonism (CI>1). This equation used Fa values from a constant ratio of drug combination to determine CI values. The resulting plot (Fa-CI) plot shows the resultant CI values bracketed by 95% confidence intervals. These Fa-CI plots are generated using the Calcusyn software. Statistically significant CI values for synergy are for example those CI value<1 with the confidence interval lines also below 1.

FIGS. 3A-3F are a series of Fa-Cl plots demonstrating combination benefit with CHOP components and Compound 44 in mutant EZH2 germinal center B-cell lymphoma cell lines. Compound 44 and doxorubicin act synergistically in the WSU-DLCL2 cells (FIG. 3A) and produce an additive effect in SU-DHL-10 cells (FIG. 3D). Combination benefit is observed with mafosfamide in WSU-DLCL2 cells (FIG. 3C) and SU-DHL-10 cells (FIG. 3F). Combination benefit is also observed with vincristine in both EZH2 Y646 mutant cell lines: WSU-DLCL2 cells (FIG. 3B) and SU-DHL-10 cells (FIG. 3E). In WSU-DLCL2 doses ranged from 0.16-20 nM for doxorubicin, 0.04-5 nM for vincristine, 0.156-10 μM for mafosfamide, and 15-1000 nM for Compound 44. In SU-DHL-10 cells doses ranged from 0.5-60 nM for doxorubicin, 0.016-2 nM for vincristine, 0.156-10 μM for mafosfamide, and 1.56-100 nM for Compound 44. Cells were treated according to pretreatment model A, and data analyzed with the Calcusyn software.

FIGS. 4A-4D are a series of plots demonstrating that glucocorticoid agonists enhance potency of Compound 44 in EZH2 mutant lymphoma lines. Potency of Compound 44 is dramatically increased when combined with glucocorticoid agonists. The addition of prednisolone (FIG. 4A, FIG. 4C) or dexamethasone (FIG. 4B, FIG. 4D) in 2 EZH2 Y646F mutant DLBCL lines according to pre-treatment model A produces a dose dependent shift in the IC₅₀ of Compound 44. Doses ranged from 15 nM-1000 nM for prednisolone and 1.5 nM-100 nM for dexamethasone in both cell lines. Doses of Compound 44 ranged from 15-1000 nM in WSU-DLCL2 cells and 1.5-100 nM in SU-DHL-10 cells.

FIGS. 5A-5D are a series of plots demonstrating combination benefit of Compound 44 with glucocorticoid agonists in EZH2 WT germinal center but not activated B-Cell lymphoma lines. Combination benefit was observed in DOHH2 EZH2 wild type GCB cells upon treatment with Compound 44 and prednisolone (FIG. 5A) or dexamethasone (FIG. 5B), according to pretreatment model A. In contrast, no combination benefit was observed in Toledo cells (in FIGS. 5C and 5D for Cpd44+ Prednisolone and Cpd44+Dexamethasone, respectively), an EZH2 wild type ABC lymphoma line. Doses ranged from 15 nM-1000 nM for prednisolone and from 1.5 nM-100 nM for dexamethasone in both cells lines. Compound 44 ranged from 0.16-10 μM in DOHH2 cells and 15.6-1000 nM in Toledo cells.

FIG. 6 is a summary table showing that Compound 44/glucocorticoid agonist combination overcomes EZH2 inhibitors (EZH2i) insensitivity in cell lines resistant to EZH2 inhibitors. Overall, a combination of prednisolone and Compound 44 leads to greater sensitivity in all GCB cell lines tested, not just EZH2i sensitive cell lines. Except for RL cells, where sequence of drug addition is crucial as preincubation with prednisolone, followed by Compound 44, is not effective.

FIGS. 7A and 7B are two plots showing very strong synergy observed in EZH2 mutant lymphoma cell line with combination of Compound 44 and other targeted therapies. Very strong synergy is observed when Compound 44 is combined with the BCL2 inhibitor Navitoclax (in FIG. 7A), as well as with mTOR inhibitor everolimus (in FIG. 7B). Dose ranges for Navitoclax are 0.16-10 μM, 0.04-5 nM for Everolimus, and 31-2000 nM for Compound 44. These data were generated in the pretreatment model A and data analyzed with Calcusyn software.

FIG. 8 is a summary table of combinations with Compound 44. Combination benefit with Compound 44 is achieved with all drugs tested in EZH2 mutant lymphoma lines. Glucocorticoid agonists demonstrate combination benefit with EZH2 WT and mutant GCB lymphoma lines, but not in an ABC lymphoma cell line.

FIGS. 9A-9C are a series of plots demonstrating that Compound 44-CHOP combinations show enhanced anti-tumor activity compared to single agents in several EZH2 mutant lymphoma xenograft models. (FIG. 9A). WSU-DLCL2 (EZH2 Y646F) xenografts were treated with Compound 44, CHOP, or the combination for 28 days, as specified in the methods. Mean tumor volumes+/− SEM are plotted. Both doses of Compound 44 at 150 mg/kg TID and 225 mg/kg BID were statistically more significant in tumor growth inhibition than vehicle alone (*p value <0.05). Treatment with Compound 44 at 225 mg/kg BID plus CHOP resulted in greater tumor regression than with any single agent alone (***p value <0.001 versus vehicle). Statistics calculated by repeated measures ANOVA. (FIG. 9B). SU-DHL6 (EZH2 Y646N) xenografts were treated with Compound 44, CHOP, or the combination for 28 days, as specified in the methods. Mean tumor volumes+/− SEM are plotted in top panel. CHOP or single agent Compound 44 alone had no effect on tumor growth, but treatment with Compound 44 at 225 mg/kg BID plus CHOP resulted in tumor growth regression during the treatment period of 28 days, while also maintaining tumor growth delay after 32 days of dosing cessation (*p value<0.0001). Survival curves (bottom panel) out to 60 days demonstrate significant tumor growth delay in animals treated with Compound 44+CHOP (**p value<0.05). Statistics calculated by two-tailed t-test. (FIG. 9C). SUDHL-10 (EZH2 Y646F) xenografts were treated with Compound 44, COP (SOC without the doxorubicin component), or the combination for 28 days, as specified in the methods. Mean tumor volumes+/− SEM are plotted in top panel. Percent survival out to 60 days in a tumor growth delay study is plotted in the middle panel (Note: 500 mg/kg and 250 mg/kg+COP survival curves are overlapping). Mean tumor weights are compared in the bottom panel, demonstrating the significant differences in tumor weight between groups (*p value <0.05, **p value <0.01, ****p value <0.0001).

FIGS. 10A-10C are panels showing that glucocorticoid target genes are up-regulated by prednisolone+Compound 44 combination in EZH2 mutant cell lines. Expression levels of (FIG. 10A). Sestrin; (FIG. 10B). TNF and (FIG. 10C) GILZ normalized to DMSO controls for each cell line with the indicated single agent or combination. Fold change values were quantified using the AACt method and RPLPO as the housekeeping gene.

FIGS. 11A and 11B are panels showing that global H3K27 acetylation and trimethylation are unaffected by prednisolone or combination treatment. Cells were treated for 4 days with increasing doses of prednisolone, Compound 44, or a combination of Compound 44+a constant dose of prednisolone. Acid extracted histones were analyzed by ELISA for H3K27me3 levels (FIG. 11A) (Prednisolone, left panel; Compound 44 and combination, right panel, with IC50 values as insets of each graph) or western blot for H3K27ac levels (FIG. 11B). For prednisolone treatment, H3K27me3 values are represented as a bar graph as there was no dose dependent changes were observed with this compound.

FIG. 12 is a western blot showing that single agent treatment with Compound 44 or prednisolone has no effect on SMARCB1 protein levels.

FIG. 13 is a scheme showing involvement of EZH2 in drug resistance to anti-VEGF therapy, which continues to be a challenge in patients with metastatic renal cell carcinoma as patients who initially respond to treatment eventually develop resistance and tumor progress.

FIG. 14 is a scheme showing the design of in vivo combination assays.

FIGS. 15A-15E are a series of plots demonstrating that inhibition of EZH2 increases sensitivity to sunitinib in ccRCC cell lines. FIGS. 15A-15B: Cell inhibition assay with single agents and combination. FIG. 15C: Combination index values indicating concentrations of sunitinib and GSK126 combination with synergy. FIGS. 15D-15E: ccRCC cell lines treated with either sunitinib, GSK126 or both for 48 hr. Bar chart indicates significant decrease in cell viability in combination treatment arm as compared to the single agents alone.

FIGS. 16A-16B are a series of plots demonstrating that knockdown of EZH2 increases sensitivity to sunitinib in ccRCC cell line. FIG. 16A: Western blot analysis showing the efficiency of EZH2 knockdown in 786-0 cell line. FIG. 16B: Specific knockdown of EZH2 in 786-0 cells are more sensitive to sunitinib as compare to the scrambled template control, 786-0_shRNA.

FIGS. 17A-17C are a series of plots demonstrating that EZH2 inhibition sensitizes tumors to sunitinib in RP-R-02LM ccRCC PDX model. Tumor growth curve shows a significant decrease in tumor growth in combination group as compared to sunitinib alone (FIGS. 17A and 17B). Body weight curve overt time indicates that mice tolerated well to both drugs and dosing schedule (FIG. 17C).

FIGS. 18A-18B are a series of plots demonstrating that combination of sunitinib and Compound B shows increased anti-metastatic effect compared to single agents alone. FIG. 18A includes representative pictures of lung tissues and H&E stain indicating a decrease in metastasis in sunitinib treated group which is increased in the combination group. There were no differences in expression of Ki67 and CD31 levels in tumor cells present in the lungs between treatment groups. FIG. 18B is a plot of number of tumor nodules in lungs with various treatments.

FIGS. 19A-19B are a series of plots demonstrating that combination of sunitinib and Compound B decreases cell proliferation in ccRCC PDX model. Decreased cell proliferation in combination treatment and Compound B treated tumors was observed in tumors at primary site as indicated Ki67 stain (FIG. 19A) and quantification (FIG. 19B). *p<0.05, **p, 0.001, ns=not significant

FIGS. 20A-20B are a series of plots demonstrating that combination of sunitinib and Compound B decreases vascular density as in ccRCC PDX model. Significant decreased in vessel density was observed was in sunitinib and combination treated group in tumors at primary site as indicated by mCD31 stain (FIG. 20A) and quantification (FIG. 20B). *p<0.05, **p<0.001, ***p<0.0001, ns=not significant

FIG. 21 is an illustration of the EZH2 protein structure.

DETAILED DESCRIPTION

The present disclosure is based partially upon the discovery that EZH2 histone methyltransferase inhibitors and other anti-cancer agents can be used in combination to treat certain tumors with superior results than those achieved by treating tumors with EZH2 histone methyltransferase inhibitors and the anti-cancer agents alone. Accordingly, the present disclosure provides a composition comprising an EZH2 histone methyltransferase inhibitor and one or more other therapeutic agents, and methods for their use to treat diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, e.g., cancer. In a certain embodiment, the present disclosure features a composition comprising a compound of Formulae (I)-(VIa) and a tyrosine kinase inhibitor such as sunitinib. In a certain embodiment, the present disclosure features a composition comprising a compound of Formulae (I)-(VIa) and an anti-VEGF agent such as sunitinib. In a certain embodiment, the present disclosure features a composition comprising a compound of Formulae (I)-(VIa) and prednisone. The present disclosure also includes methods for combination therapies comprising EZH2 histone methyltransferase inhibitor and one or more therapeutic agents, such as a compound of Formulae (I)-(VIa) and sunitinib or prednisone, to treat cancer, e.g., renal cell carcinoma, follicular lymphoma (FL) and diffuse cell large B-cell lymphoma (DCLBL). Specifically, the methods of the present disclosure are useful for treating or preventing cancer or inhibiting cancer cell proliferation.

EZH2 is a histone methyltransferase that is the catalytic subunit of the PRC2 complex which catalyzes the mono- through tri-methylation of lysine 27 on histone H3 (H3-K27). Histone H3-K27 trimethylation is a mechanism for suppressing transcription of specific genes that are proximal to the site of histone modification. This trimethylation is known to be a cancer marker with altered expression in cancer, such as prostate cancer (see, e.g., U.S. Patent Application Publication No. 2003/0175736; incorporated herein by reference in its entirety). Other studies provided evidence for a functional link between dysregulated EZH2 expression, transcriptional repression, and neoplastic transformation. Varambally et al. (2002) Nature 419(6907):624-9 Kleer et al. (2003) Proc Natl Acad Sci USA 100(20):11606-11.

Response to anti-VEGF therapy continues to be a challenge in patients with metastatic renal cell carcinoma as patients who initially respond to treatment eventually develop resistance and progress. Epigenetic changes such as the overexpression of Enhancer of zeste homologue (EZH2) which is a histone methyltransferase has been shown to be frequently overexpressed in human malignances, involved in epigenetic silencing of a number of genes and the regulation tumor angiogenesis. EZH2 has been recently reported to be involved in drug resistance. See, e.g., Herranz, Nicolás, et al. “Polycomb complex 2 is required for E-cadherin repression by the Snaill transcription factor.” Molecular and cellular biology 28.15 (2008): 4772-4781; and Adelaiye, Remi, et al. “Sunitinib dose-escalation overcomes transient resistance in clear cell renal cell carcinoma and is associated with epigenetic modifications.” Molecular cancer therapeutics (2014): molcanther-0208. Accordingly, inhibition of EZH2 can re-sensitize tumors to anti-VEGF agents.

An aspect of the present disclosure relates to methods for treating or alleviating a symptom of cancer or precancerous condition in a subject by administering to a subject expressing a mutant EZH2 a therapeutically effective amount of an EZH2 inhibitor and one or more other therapeutic agents (such as a tyrosine kinase inhibitor or an anti-VEGF agent). The mutant EZH2 of the present disclosure refers to a mutant EZH2 polypeptide or a nucleic acid sequence encoding a mutant EZH2 polypeptide. In certain embodiments the mutant EZH2 comprises one or more mutations in its substrate pocket domain as defined in SEQ ID NO: 6. For example, the mutation may be a substitution, a point mutation, a nonsense mutation, a misssense mutation, a deletion, or an insertion.

Human EZH2 nucleic acids and polypeptides have previously been described. See, e.g., Chen et al. (1996) Genomics 38:30-7 [746 amino acids]; Swiss-Prot Accession No. Q15910 [746 amino acids]; GenBank Accession Nos. NM_004456 and NP_004447 (isoform a [751 amino acids]); and GenBank Accession Nos. NM_152998 and NP_694543 (isoform b [707 amino acids]), each of which is incorporated herein by reference in its entirety.

Amino acid sequence of human EZH2 (Swiss-Prot Accession No. Q15910) (SEQ ID NO: 1) MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKIL ERTEILNQEWKQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKT LNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELI KNYDGKVHGDRECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQ KDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQ QLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRP GGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEK KDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDN FCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTPPRKKKRKHRLWA AHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCS SECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDE ADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVM MVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP Nucleotide sequence of human EZH2, transcript variant 1 (GenBank Accession No. NM_004456) (SEQ ID NO: 2) ggcggcgcttgattgggctgggggggccaaataaaagcgatggcgattgg gctgccgcgtttggcgctcggtccggtcgcgtccgacacccggtgggact cagaaggcagtggagccccggcggcggcggcggcggcgcgcgggggcgac gcgcgggaacaacgcgagtcggcgcgcgggacgaagaataatcatgggcc agactgggaagaaatctgagaagggaccagtttgttggcggaagcgtgta aaatcagagtacatgcgactgagacagctcaagaggttcagacgagctga tgaagtaaagagtatgtttagttccaatcgtcagaaaattttggaaagaa cggaaatcttaaaccaagaatggaaacagcgaaggatacagcctgtgcac atcctgacttctgtgagctcattgcgcgggactagggagtgttcggtgac cagtgacttggattttccaacacaagtcatcccattaaagactctgaatg cagttgcttcagtacccataatgtattcttggtctcccctacagcagaat tttatggtggaagatgaaactgttttacataacattccttatatgggaga tgaagttttagatcaggatggtactttcattgaagaactaataaaaaatt atgatgggaaagtacacggggatagagaatgtgggtttataaatgatgaa atttttgtggagttggtgaatgcccttggtcaatataatgatgatgacga tgatgatgatggagacgatcctgaagaaagagaagaaaagcagaaagatc tggaggatcaccgagatgataaagaaagccgcccacctcggaaatttcct tctgataaaatttttgaagccatttcctcaatgtttccagataagggcac agcagaagaactaaaggaaaaatataaagaactcaccgaacagcagctcc caggcgcacttcctcctgaatgtacccccaacatagatggaccaaatgct aaatctgttcagagagagcaaagcttacactcctttcatacgcttttctg taggcgatgttttaaatatgactgcttcctacatcgtaagtgcaattatt cttttcatgcaacacccaacacttataagcggaagaacacagaaacagct ctagacaacaaaccttgtggaccacagtgttaccagcatttggagggagc aaaggagtttgctgctgctctcaccgctgagcggataaagaccccaccaa aacgtccaggaggccgcagaagaggacggcttcccaataacagtagcagg cccagcacccccaccattaatgtgctggaatcaaaggatacagacagtga tagggaagcagggactgaaacggggggagagaacaatgataaagaagaag aagagaagaaagatgaaacttcgagctcctctgaagcaaattctcggtgt caaacaccaataaagatgaagccaaatattgaacctcctgagaatgtgga gtggagtggtgctgaagcctcaatgtttagagtcctcattggcacttact atgacaatttctgtgccattgctaggttaattgggaccaaaacatgtaga caggtgtatgagtttagagtcaaagaatctagcatcatagctccagctcc cgctgaggatgtggatactcctccaaggaaaaagaagaggaaacaccggt tgtgggctgcacactgcagaaagatacagctgaaaaaggacggctcctct aaccatgtttacaactatcaaccctgtgatcatccacggcagccttgtga cagttcgtgcccttgtgtgatagcacaaaatttttgtgaaaagttttgtc aatgtagttcagagtgtcaaaaccgctttccgggatgccgctgcaaagca cagtgcaacaccaagcagtgcccgtgctacctggctgtccgagagtgtga ccctgacctctgtcttacttgtggagccgctgaccattgggacagtaaaa atgtgtcctgcaagaactgcagtattcagcggggctccaaaaagcatcta ttgctggcaccatctgacgtggcaggctgggggatttttatcaaagatcc tgtgcagaaaaatgaattcatctcagaatactgtggagagattatttctc aagatgaagctgacagaagagggaaagtgtatgataaatacatgtgcagc tttctgttcaacttgaacaatgattttgtggtggatgcaacccgcaaggg taacaaaattcgttttgcaaatcattcggtaaatccaaactgctatgcaa aagttatgatggttaacggtgatcacaggataggtatttttgccaagaga gccatccagactggcgaagagctgttttttgattacagatacagccaggc tgatgccctgaagtatgtcggcatcgaaagagaaatggaaatcccttgac atctgctacctcctcccccctcctctgaaacagctgccttagcttcagga acctcgagtactgtgggcaatttagaaaaagaacatgcagtttgaaattc tgaatttgcaaagtactgtaagaataatttatagtaatgagtttaaaaat caactttttattgccttctcaccagctgcaaagtgttttgtaccagtgaa tttttgcaataatgcagtatggtacatttttcaactttgaataaagaata cttgaacttgtccttgttgaatc Full amino acid sequence of EZH2, isoform a (GenBank Accession No. NP_004447) (SEQ ID NO: 3) MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKIL ERTEILNQEWKQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKT LNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELI KNYDGKVHGDRECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQ KDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQ QLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHRKC NYSFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKT PPKRPGGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDK EEEEKKDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIG TYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTPPRKKKRK HRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEK FCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWD SKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEI ISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNC YAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIER EMEIP Nucleotide sequence of human EZH2, transcript variant 2 (GenBank Accession No. NM_152998) (SEQ ID NO: 4) ggcggcgcttgattgggctgggggggccaaataaaagcgatggcgattgg gctgccgcgtttggcgctcggtccggtcgcgtccgacacccggtgggact cagaaggcagtggagccccggcggcggcggcggcggcgcgcgggggcgac gcgcgggaacaacgcgagtcggcgcgcgggacgaagaataatcatgggcc agactgggaagaaatctgagaagggaccagtttgttggcggaagcgtgta aaatcagagtacatgcgactgagacagctcaagaggttcagacgagctga tgaagtaaagagtatgtttagttccaatcgtcagaaaattttggaaagaa cggaaatcttaaaccaagaatggaaacagcgaaggatacagcctgtgcac atcctgacttctgtgagctcattgcgcgggactagggaggtggaagatga aactgttttacataacattccttatatgggagatgaagttttagatcagg atggtactttcattgaagaactaataaaaaattatgatgggaaagtacac ggggatagagaatgtgggtttataaatgatgaaatttttgtggagttggt gaatgcccttggtcaatataatgatgatgacgatgatgatgatggagacg atcctgaagaaagagaagaaaagcagaaagatctggaggatcaccgagat gataaagaaagccgcccacctcggaaatttccttctgataaaatttttga agccatttcctcaatgtttccagataagggcacagcagaagaactaaagg aaaaatataaagaactcaccgaacagcagctcccaggcgcacttcctcct gaatgtacccccaacatagatggaccaaatgctaaatctgttcagagaga gcaaagcttacactcctttcatacgcttttctgtaggcgatgttttaaat atgactgcttcctacatccttttcatgcaacacccaacacttataagcgg aagaacacagaaacagctctagacaacaaaccttgtggaccacagtgtta ccagcatttggagggagcaaaggagtttgctgctgctctcaccgctgagc ggataaagaccccaccaaaacgtccaggaggccgcagaagaggacggctt cccaataacagtagcaggcccagcacccccaccattaatgtgctggaatc aaaggatacagacagtgatagggaagcagggactgaaacggggggagaga acaatgataaagaagaagaagagaagaaagatgaaacttcgagctcctct gaagcaaattctcggtgtcaaacaccaataaagatgaagccaaatattga acctcctgagaatgtggagtggagtggtgctgaagcctcaatgtttagag tcctcattggcacttactatgacaatttctgtgccattgctaggttaatt gggaccaaaacatgtagacaggtgtatgagtttagagtcaaagaatctag catcatagctccagctcccgctgaggatgtggatactcctccaaggaaaa agaagaggaaacaccggttgtgggctgcacactgcagaaagatacagctg aaaaaggacggctcctctaaccatgtttacaactatcaaccctgtgatca tccacggcagccttgtgacagttcgtgcccttgtgtgatagcacaaaatt tttgtgaaaagttttgtcaatgtagttcagagtgtcaaaaccgctttccg ggatgccgctgcaaagcacagtgcaacaccaagcagtgcccgtgctacct ggctgtccgagagtgtgaccctgacctctgtcttacttgtggagccgctg accattgggacagtaaaaatgtgtcctgcaagaactgcagtattcagcgg ggctccaaaaagcatctattgctggcaccatctgacgtggcaggctgggg gatttttatcaaagatcctgtgcagaaaaatgaattcatctcagaatact gtggagagattatttctcaagatgaagctgacagaagagggaaagtgtat gataaatacatgtgcagctttctgttcaacttgaacaatgattttgtggt ggatgcaacccgcaagggtaacaaaattcgttttgcaaatcattcggtaa atccaaactgctatgcaaaagttatgatggttaacggtgatcacaggata ggtatttttgccaagagagccatccagactggcgaagagctgttttttga ttacagatacagccaggctgatgccctgaagtatgtcggcatcgaaagag aaatggaaatcccttgacatctgctacctcctcccccctcctctgaaaca gctgccttagcttcaggaacctcgagtactgtgggcaatttagaaaaaga acatgcagtttgaaattctgaatttgcaaagtactgtaagaataatttat agtaatgagtttaaaaatcaactttttattgccttctcaccagctgcaaa gtgttttgtaccagtgaatttttgcaataatgcagtatggtacatttttc aactttgaataaagaatacttgaacttgtccttgttgaatc Full amino acid sequence of EZH2, isoform b (GenBank Accession No. NP_694543) (SEQ ID NO: 5) MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKIL ERTEILNQEWKQRRIQPVHILTSVSSLRGTREVEDETVLHNIPYMGDEVL DQDGTFIEELIKNYDGKVHGDRECGFINDEIFVELVNALGQYNDDDDDDD GDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEE LKEKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRC FKYDCFLHPFHATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALT AERIKTPPKRPGGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETG GENNDKEEEEKKDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASM FRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTPP RKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIA QNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCG AADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFIS EYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANH SVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGI EREMEIP Full amino acid sequence of EZH2, isoform e (GenBank Accession No. NP_001190178.1) (SEQ ID NO: 11) MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKIL ERTEILNQEWKQRRIQPVHILTSCSVTSDLDFPTQVIPLKTLNAVASVPI MYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHG DRECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQKDLEDHRDD KESRPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQQLPGALPPE CTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNTYKRK NTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLP NNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEKKDETSSSSE ANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIG TKTCRQVYEFRVKESSIIAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLK KGQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSC KNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEA DRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMM VNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP Homo sapiens enhancer of zeste homolog 2 (Drosophila) (EZH2), transcript variant 5, nucleotide sequence (GenBank Accession No. NM_001203249.1) (SEQ ID NO: 12) GACGACGTTCGCGGCGGGGAACTCGGAGTAGCTTCGCCTCTGACGTTTCC CCACGACGCACCCCGAAATCCCCCTGAGCTCCGGCGGTCGCGGGCTGCCC TCGCCGCCTGGTCTGGCTTTATGCTAAGTTTGAGGGAAGAGTCGAGCTGC TCTGCTCTCTATTGATTGTGTTTCTGGAGGGCGTCCTGTTGAATTCCCAC TTCATTGTGTACATCCCCTTCCGTTCCCCCCAAAAATCTGTGCCACAGGG TTACTTTTTGAAAGCGGGAGGAATCGAGAAGCACGATCTTTTGGAAAACT TGGTGAACGCCTAAATAATCATGGGCCAGACTGGGAAGAAATCTGAGAAG GGACCAGTTTGTTGGCGGAAGCGTGTAAAATCAGAGTACATGCGACTGAG ACAGCTCAAGAGGTTCAGACGAGCTGATGAAGTAAAGAGTATGTTTAGTT CCAATCGTCAGAAAATTTTGGAAAGAACGGAAATCTTAAACCAAGAATGG AAACAGCGAAGGATACAGCCTGTGCACATCCTGACTTCTTGTTCGGTGAC CAGTGACTTGGATTTTCCAACACAAGTCATCCCATTAAAGACTCTGAATG CAGTTGCTTCAGTACCCATAATGTATTCTTGGTCTCCCCTACAGCAGAAT TTTATGGTGGAAGATGAAACTGTTTTACATAACATTCCTTATATGGGAGA TGAAGTTTTAGATCAGGATGGTACTTTCATTGAAGAACTAATAAAAAATT ATGATGGGAAAGTACACGGGGATAGAGAATGTGGGTTTATAAATGATGAA ATTTTTGTGGAGTTGGTGAATGCCCTTGGTCAATATAATGATGATGACGA TGATGATGATGGAGACGATCCTGAAGAAAGAGAAGAAAAGCAGAAAGATC TGGAGGATCACCGAGATGATAAAGAAAGCCGCCCACCTCGGAAATTTCCT TCTGATAAAATTTTTGAAGCCATTTCCTCAATGTTTCCAGATAAGGGCAC AGCAGAAGAACTAAAGGAAAAATATAAAGAACTCACCGAACAGCAGCTCC CAGGCGCACTTCCTCCTGAATGTACCCCCAACATAGATGGACCAAATGCT AAATCTGTTCAGAGAGAGCAAAGCTTACACTCCTTTCATACGCTTTTCTG TAGGCGATGTTTTAAATATGACTGCTTCCTACATCCTTTTCATGCAACAC CCAACACTTATAAGCGGAAGAACACAGAAACAGCTCTAGACAACAAACCT TGTGGACCACAGTGTTACCAGCATTTGGAGGGAGCAAAGGAGTTTGCTGC TGCTCTCACCGCTGAGCGGATAAAGACCCCACCAAAACGTCCAGGAGGCC GCAGAAGAGGACGGCTTCCCAATAACAGTAGCAGGCCCAGCACCCCCACC ATTAATGTGCTGGAATCAAAGGATACAGACAGTGATAGGGAAGCAGGGAC TGAAACGGGGGGAGAGAACAATGATAAAGAAGAAGAAGAGAAGAAAGATG AAACTTCGAGCTCCTCTGAAGCAAATTCTCGGTGTCAAACACCAATAAAG ATGAAGCCAAATATTGAACCTCCTGAGAATGTGGAGTGGAGTGGTGCTGA AGCCTCAATGTTTAGAGTCCTCATTGGCACTTACTATGACAATTTCTGTG CCATTGCTAGGTTAATTGGGACCAAAACATGTAGACAGGTGTATGAGTTT AGAGTCAAAGAATCTAGCATCATAGCTCCAGCTCCCGCTGAGGATGTGGA TACTCCTCCAAGGAAAAAGAAGAGGAAACACCGGTTGTGGGCTGCACACT GCAGAAAGATACAGCTGAAAAAGGGTCAAAACCGCTTTCCGGGATGCCGC TGCAAAGCACAGTGCAACACCAAGCAGTGCCCGTGCTACCTGGCTGTCCG AGAGTGTGACCCTGACCTCTGTCTTACTTGTGGAGCCGCTGACCATTGGG ACAGTAAAAATGTGTCCTGCAAGAACTGCAGTATTCAGCGGGGCTCCAAA AAGCATCTATTGCTGGCACCATCTGACGTGGCAGGCTGGGGGATTTTTAT CAAAGATCCTGTGCAGAAAAATGAATTCATCTCAGAATACTGTGGAGAGA TTATTTCTCAAGATGAAGCTGACAGAAGAGGGAAAGTGTATGATAAATAC ATGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAAC CCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACT GCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATAGGTATTTTT GCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATA CAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAA TCCCTTGACATCTGCTACCTCCTCCCCCCTCCTCTGAAACAGCTGCCTTA GCTTCAGGAACCTCGAGTACTGTGGGCAATTTAGAAAAAGAACATGCAGT TTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAG TTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGT ACCAGTGAATTTTTGCAATAATGCAGTATGGTACATTTTTCAACTTTGAA TAAAGAATACTTGAACTTGTCCTTGTTGAATC

A structure model of partial EZH2 protein based on the A chain of nuclear receptor binding SET domain protein 1 (NSD1) is provided below. This model corresponds to amino acid residues 533-732 of EZH2 sequence of SEQ ID NO: 1.

The corresponding amino acid sequence of this structure model is provided below. The residues in the substrate pocket domain are underlined. The residues in the SET domain are shown italic.

(SEQ ID NO: 6)

The catalytic site of EZH2 is believed to reside in a conserved domain of the protein known as the SET domain. The amino acid sequence of the SET domain of EZH2 is provided by the following partial sequence spanning amino acid residues 613-726 of Swiss-Prot Accession No. Q15910 (SEQ ID NO: 1):

(SEQ ID NO: 7) HLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDKYM CSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFA KRAIQTGEELFFDY. The tyrosine (Y) residue shown underlined in SEQ ID NO: 7 is Tyr641 (Y641) in Swiss-Prot Accession No. Q15910 (SEQ ID NO: 1).

The SET domain of GenBank Accession No. NP_004447 (SEQ ID NO: 3) spans amino acid residues 618-731 and is identical to SEQ ID NO:6. The tyrosine residue corresponding to Y641 in Swiss-Prot Accession No. Q15910 shown underlined in SEQ ID NO: 7 is Tyr646 (Y646) in GenBank Accession No. NP_004447 (SEQ ID NO: 3).

The SET domain of GenBank Accession No. NP_694543 (SEQ ID NO: 5) spans amino acid residues 574-687 and is identical to SEQ ID NO: 7. The tyrosine residue corresponding to Y641 in Swiss-Prot Accession No. Q15910 shown underlined in SEQ ID NO: 7 is Tyr602 (Y602) in GenBank Accession No. NP_694543 (SEQ ID NO: 5).

The nucleotide sequence encoding the SET domain of GenBank Accession No. NP_004447 is

(SEQ ID NO: 8) catctattgctggcaccatctgacgtggcaggctgggggatttttatcaa agatcctgtgcagaaaaatgaattcatctcagaatactgtggagagatta tttctcaagatgaagctgacagaagagggaaagtgtatgataaatacatg tgcagctttctgttcaacttgaacaatgattttgtggtggatgcaacccg caagggtaacaaaattcgttttgcaaatcattcggtaaatccaaactgct atgcaaaagttatgatggttaacggtgatcacaggataggtatttttgcc aagagagccatccagactggcgaagagctgttttttgattac, where the codon encoding Y641 is shown underlined.

For purposes of this application, amino acid residue Y641 of human EZH2 is to be understood to refer to the tyrosine residue that is or corresponds to Y641 in Swiss-Prot Accession No. Q15910.

Full amino acid sequence of Y641 mutant EZH2 (SEQ ID NO: 9) MGQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKIL ERTEILNQEWKQRRIQPVHILTSVSSLRGTRECSVTSDLDFPTQVIPLKT LNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELI KNYDGKVHGDRECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQ KDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELKEKYKELTEQ QLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFH ATPNTYKRKNTETALDNKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRP GGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKEEEEK KDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDN FCAIARLIGTKTCRQVYEFRVKESSIIAPAPAEDVDTPPRKKKRKHRLWA AHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCS SECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVS CKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEXCGEIISQDE ADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVM MVNGDHRIGIFAKRAIQTGEELFFDYRYSQADALKYVGIEREMEIP Wherein x can be any amino acid residue other than tyrosine (Y)

Also for purposes of this application, a Y641 mutant of human EZH2, and, equivalently, a Y641 mutant of EZH2, is to be understood to refer to a human EZH2 in which the amino acid residue corresponding to Y641 of wild-type human EZH2 is substituted by an amino acid residue other than tyrosine.

In one embodiment the amino acid sequence of a Y641 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of a single amino acid residue corresponding to Y641 of wild-type human EZH2 by an amino acid residue other than tyrosine.

In one embodiment the amino acid sequence of a Y641 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of phenylalanine (F) for the single amino acid residue corresponding to Y641 of wild-type human EZH2. The Y641 mutant of EZH2 according to this embodiment is referred to herein as a Y641F mutant or, equivalently, Y641F.

In one embodiment the amino acid sequence of a Y641 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of histidine (H) for the single amino acid residue corresponding to Y641 of wild-type human EZH2. The Y641 mutant of EZH2 according to this embodiment is referred to herein as a Y641H mutant or, equivalently, Y641H.

In one embodiment the amino acid sequence of a Y641 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of asparagine (N) for the single amino acid residue corresponding to Y641 of wild-type human EZH2. The Y641 mutant of EZH2 according to this embodiment is referred to herein as a Y641N mutant or, equivalently, Y641N.

In one embodiment the amino acid sequence of a Y641 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of serine (S) for the single amino acid residue corresponding to Y641 of wild-type human EZH2. The Y641 mutant of EZH2 according to this embodiment is referred to herein as a Y641S mutant or, equivalently, Y641S.

In one embodiment the amino acid sequence of a Y641 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of cysteine (C) for the single amino acid residue corresponding to Y641 of wild-type human EZH2. The Y641 mutant of EZH2 according to this embodiment is referred to herein as a Y641C mutant or, equivalently, Y641C.

In one embodiment the amino acid sequence of a A677 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of a non-alanine amino acid, preferably glycine (G) for the single amino acid residue corresponding to A677 of wild-type human EZH2. The A677 mutant of EZH2 according to this embodiment is referred to herein as an A677 mutant, and preferably an A677G mutant or, equivalently, A677G.

In one embodiment the amino acid sequence of a A687 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of a non-alanine amino acid, preferably valine (V) for the single amino acid residue corresponding to A687 of wild-type human EZH2. The A687 mutant of EZH2 according to this embodiment is referred to herein as an A687 mutant and preferably an A687V mutant or, equivalently, A687V.

In one embodiment the amino acid sequence of a R685 mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 only by substitution of a non-arginine amino acid, preferably histidine (H) or cysteine (C) for the single amino acid residue corresponding to R685 of wild-type human EZH2. The R685 mutant of EZH2 according to this embodiment is referred to herein as an R685 mutant and preferably an R685C mutant or an R685H mutant or, equivalently, R685H or R685C.

In one embodiment the amino acid sequence of a mutant of EZH2 differs from the amino acid sequence of wild-type human EZH2 in one or more amino acid residues in its substrate pocket domain as defined in SEQ ID NO: 6. The mutant of EZH2 according to this embodiment is referred to herein as an EZH2 mutant.

Other exemplary substitution amino acid mutation includes a substitution at amino acid position 677, 687, 674, 685, or 641 of SEQ ID NO: 1, such as, but is not limited to a substitution of glycine (G) for the wild type residue alanine (A) at amino acid position 677 of SEQ ID NO: 1 (A677G); a substitution of valine (V) for the wild type residue alanine (A) at amino acid position 687 of SEQ ID NO: 1 (A687V); a substitution of methionine (M) for the wild type residue valine (V) at amino acid position 674 of SEQ ID NO: 1 (V674M); a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 685 of SEQ ID NO: 1 (R685H); a substitution of cysteine (C) for the wild type residue arginine (R) at amino acid position 685 of SEQ ID NO: 1 (R685C); a substitution of phenylalanine (F) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641F); a substitution of histidine (H) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641H); a substitution of asparagine (N) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641N); a substitution of serine (S) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641S); or a substitution of cysteine (C) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO: 1 (Y641C).

The mutation of the present disclosure may also include a substitution of serine (S) for the wild type residue asparagine (N) at amino acid position 322 of SEQ ID NO: 3 (N322S), a substitution of glutamine (Q) for the wild type residue arginine (R) at amino acid position 288 of SEQ ID NO: 3 (R288Q), a substitution of isoleucine (I) for the wild type residue threonine (T) at amino acid position 573 of SEQ ID NO: 3 (T5731), a substitution of glutamic acid (E) for the wild type residue aspartic acid (D) at amino acid position 664 of SEQ ID NO: 3 (D664E), a substitution of glutamine (Q) for the wild type residue arginine (R) at amino acid position 458 of SEQ ID NO: 5 (R458Q), a substitution of lysine (K) for the wild type residue glutamic acid (E) at amino acid position 249 of SEQ ID NO: 3 (E249K), a substitution of cysteine (C) for the wild type residue arginine (R) at amino acid position 684 of SEQ ID NO: 3 (R684C), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 628 of SEQ ID NO: 11 (R628H), a substitution of histidine (H) for the wild type residue glutamine (Q) at amino acid position 501 of SEQ ID NO: 5 (Q501H), a substitution of asparagine (N) for the wild type residue aspartic acid (D) at amino acid position 192 of SEQ ID NO: 3 (D192N), a substitution of valine (V) for the wild type residue aspartic acid (D) at amino acid position 664 of SEQ ID NO: 3 (D664V), a substitution of leucine (L) for the wild type residue valine (V) at amino acid position 704 of SEQ ID NO: 3 (V704L), a substitution of serine (S) for the wild type residue proline (P) at amino acid position 132 of SEQ ID NO: 3 (P132S), a substitution of lysine (K) for the wild type residue glutamic acid (E) at amino acid position 669 of SEQ ID NO: 11 (E669K), a substitution of threonine (T) for the wild type residue alanine (A) at amino acid position 255 of SEQ ID NO: 3 (A255T), a substitution of valine (V) for the wild type residue glutamic acid (E) at amino acid position 726 of SEQ ID NO: 3 (E726V), a substitution of tyrosine (Y) for the wild type residue cysteine (C) at amino acid position 571 of SEQ ID NO: 3 (C571Y), a substitution of cysteine (C) for the wild type residue phenylalanine (F) at amino acid position 145 of SEQ ID NO: 3 (F145C), a substitution of threonine (T) for the wild type residue asparagine (N) at amino acid position 693 of SEQ ID NO: 3 (N693T), a substitution of serine (S) for the wild type residue phenylalanine (F) at amino acid position 145 of SEQ ID NO: 3 (F145S), a substitution ofhistidine (H) for the wild type residue glutamine (Q) at amino acid position 109 of SEQ ID NO: 11 (Q109H), a substitution of cysteine (C) for the wild type residue phenylalanine (F) at amino acid position 622 of SEQ ID NO: 11 (F622C), a substitution of arginine (R) for the wild type residue glycine (G) at amino acid position 135 of SEQ ID NO: 3 (G135R), a substitution of glutamine (Q) for the wild type residue arginine (R) at amino acid position 168 of SEQ ID NO: 5 (R168Q), a substitution of arginine (R) for the wild type residue glycine (G) at amino acid position 159 of SEQ ID NO: 3 (G159R), a substitution of cysteine (C) for the wild type residue arginine (R) at amino acid position 310 of SEQ ID NO: 5 (R310C), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 561 of SEQ ID NO: 3 (R561H), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 634 of SEQ ID NO: 11 (R634H), a substitution of arginine (R) for the wild type residue glycine (G) at amino acid position 660 of SEQ ID NO: 3 (G660R), a substitution of cysteine (C) for the wild type residue tyrosine (Y) at amino acid position 181 of SEQ ID NO: 3 (Y181C), a substitution of arginine (R) for the wild type residue histidine (H) at amino acid position 297 of SEQ ID NO: 3 (H297R), a substitution of serine (S) for the wild type residue cysteine (C) at amino acid position 612 of SEQ ID NO: 11 (C612S), a substitution of tyrosine (Y) for the wild type residue histidine (H) at amino acid position 694 of SEQ ID NO: 3 (H694Y), a substitution of alanine (A) for the wild type residue aspartic acid (D) at amino acid position 664 of SEQ ID NO: 3 (D664A), a substitution of threonine (T) for the wild type residue isoleucine (I) at amino acid position 150 of SEQ ID NO: 3 (I150T), a substitution of arginine (R) for the wild type residue isoleucine (I) at amino acid position 264 of SEQ ID NO: 3 (1264R), a substitution of leucine (L) for the wild type residue proline (P) at amino acid position 636 of SEQ ID NO: 3 (P636L), a substitution of threonine (T) for the wild type residue isoleucine (I) at amino acid position 713 of SEQ ID NO: 3 (I713T), a substitution of proline (P) for the wild type residue glutamine (Q) at amino acid position 501 of SEQ ID NO: 5 (Q501P), a substitution of glutamine (Q) for the wild type residue lysine (K) at amino acid position 243 of SEQ ID NO: 3 (K243Q), a substitution of aspartic acid (D) for the wild type residue glutamic acid (E) at amino acid position 130 of SEQ ID NO: 5 (E130D), a substitution of glycine (G) for the wild type residue arginine (R) at amino acid position 509 of SEQ ID NO: 3 (R509G), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 566 of SEQ ID NO: 3 (R566H), a substitution of histidine (H) for the wild type residue aspartic acid (D) at amino acid position 677 of SEQ ID NO: 3 (D677H), a substitution of asparagine (N) for the wild type residue lysine (K) at amino acid position 466 of SEQ ID NO: 5 (K466N), a substitution of histidine (H) for the wild type residue arginine (R) at amino acid position 78 of SEQ ID NO: 3 (R78H), a substitution of methionine (M) for the wild type residue lysine (K) at amino acid position 1 of SEQ ID NO: 6 (K6M), a substitution of leucine (L) for the wild type residue serine (S) at amino acid position 538 of SEQ ID NO: 3 (S538L), a substitution of glutamine (Q) for the wild type residue leucine (L) at amino acid position 149 of SEQ ID NO: 3 (L149Q), a substitution of valine (V) for the wild type residue leucine (L) at amino acid position 252 of SEQ ID NO: 3 (L252V), a substitution of valine (V) for the wild type residue leucine (L) at amino acid position 674 of SEQ ID NO: 3 (L674V), a substitution of valine (V) for the wild type residue alanine (A) at amino acid position 656 of SEQ ID NO: 3 (A656V), a substitution of aspartic acid (D) for the wild type residue alanine (A) at amino acid position 731 of SEQ ID NO: 3 (Y731D), a substitution of threonine (T) for the wild type residue alanine (A) at amino acid position 345 of SEQ ID NO: 3 (A345T), a substitution of aspartic acid (D) for the wild type residue alanine (A) at amino acid position 244 of SEQ ID NO: 3 (Y244D), a substitution of tryptophan (W) for the wild type residue cysteine (C) at amino acid position 576 of SEQ ID NO: 3 (C576W), a substitution of lysine (K) for the wild type residue asparagine (N) at amino acid position 640 of SEQ ID NO: 3 (N640K), a substitution of lysine (K) for the wild type residue asparagine (N) at amino acid position 675 of SEQ ID NO: 3 (N675K), a substitution of tyrosine (Y) for the wild type residue aspartic acid (D) at amino acid position 579 of SEQ ID NO: 11 (D579Y), a substitution of isoleucine (I) for the wild type residue asparagine (N) at amino acid position 693 of SEQ ID NO: 3 (N693I), and a substitution of lysine (K) for the wild type residue asparagine (N) at amino acid position 693 of SEQ ID NO: 3 (N693K).

The mutation of the present disclosure may be a frameshift at amino acid position 730, 391, 461, 441, 235, 254, 564, 662, 715, 405, 685, 64, 73, 656, 718, 374, 592, 505, 730, or 363 of SEQ ID NO: 3, 5 or 11 or the corresponding nucleotide position of the nucleic acid sequence encoding SEQ ID NO: 3, 5, or 21. The mutation of the EZH2 may also be an insertion of a glutamic acid (E) between amino acid positions 148 and 149 of SEQ ID NO: 3, 5 or 11. Another example of EZH2 mutation is a deletion of glutamic acid (E) and leucine (L) at amino acid positions 148 and 149 of SEQ ID NO: 3, 5 or 11. The mutant EZH2 may further comprise a nonsense mutation at amino acid position 733, 25, 317, 62, 553, 328, 58, 207, 123, 63, 137, or 60 of SEQ ID NO: 3, 5 or 11.

Cells heterozygous for EZH2 would be expected to display a malignant phenotype due to the efficient formation of H3-K27me1 by the WT enzyme and the efficient, subsequent transition of this progenitor species to H3-K27me2, and, especially, H3-K27me3, by the mutant enzyme form(s).

Previous results point to dependency on enzymatic coupling between enzymes that perform H3-K27 mono-methylation and certain mutant forms of EZH2 for pathogenesis in follicular lymphoma and diffuse large B-cell lymphoma. For example, cells expressing Y641 mutant EZH2 may be more sensitive to small molecule EZH2 inhibitors than cells expressing WT EZH2. Specifically, cells expressing Y641 mutant EZH2 show reduced growing, dividing or proliferation, or even undergo apoptosis or necrosis after the treatment of EZH2 inhibitors. In contrast, cells expressing WT EZH2 are not responsive to the anti-proliferative effect of the EZH2 inhibitors (U.S. patent application Ser. No. 13/230,703 (now U.S. Pat. No. 8,895,245); incorporated herein by reference in its entirety.)

An aspect of the present disclosure is a method for treating or alleviating a symptom of cancer or precancerous condition in a subject by administering to a subject expressing a mutant EZH2 comprising a mutation in the substrate pocket domain as defined in SEQ ID NO: 6 a therapeutically effective amount of an EZH2 inhibitor as described herein, e.g., a compound of Formulae (I)-(VIa) in combination with another agent suitable to be administered together simultaneously, sequentially, or in alternation.

Another aspect of the disclosure is a method for inhibiting in a subject conversion of H3-K27 to trimethylated H3-K27. The inhibition can involve inhibiting in a subject conversion of unmethylated H3-K27 to monomethylated H3-K27, conversion of monomethylated H3-K27 to dimethylated H3-K27, conversion of dimethylated H3-K27 to trimethylated H3-K27, or any combination thereof, including, for example, conversion of monomethylated H3-K27 to dimethylated H3-K27 and conversion of dimethylated H3-K27 to trimethylated H3-K27. As used herein, unmethylated H3-K27 refers to histone H3 with no methyl group covalently linked to the amino group of lysine 27. As used herein, monomethylated H3-K27 refers to histone H3 with a single methyl group covalently linked to the amino group of lysine 27. Monomethylated H3-K27 is also referred to herein as H3-K27me1. As used herein, dimethylated H3-K27 refers to histone H3 with two methyl groups covalently linked to the amino group of lysine 27. Dimethylated H3-K27 is also referred to herein as H3-K27me2. As used herein, trimethylated H3-K27 refers to histone H3 with three methyl groups covalently linked to the amino group of lysine 27. Trimethylated H3-K27 is also referred to herein as H3-K27me3.

Histone H3 is a 136 amino acid long protein, the sequence of which is known. See, for example, GenBank Accession No. CAB02546, the content of which is incorporated herein by reference. As disclosed further herein, in addition to full-length histone H3, peptide fragments of histone H3 comprising the lysine residue corresponding to K27 of full-length histone H3 can be used as substrate for EZH2 (and likewise for mutant forms of EZH2) to assess conversion of H3-K27m1 to H3-K27m2 and conversion of H3-K27m2 to H3-K27m3. In one embodiment, such peptide fragment corresponds to amino acid residues 21-44 of histone H3. Such peptide fragment has the amino acid sequence

(SEQ ID NO: 10) LATKAARKSAPATGGVKKPHRYRP.

A composition of the present disclosure comprises a compound of Formulae (I)-(VIa) and one or more other therapeutic agents, or a pharmaceutically acceptable salt thereof. The compounds of Formulae (I)-(VIa) are suitable for administration as part of a combination therapy with one or more other therapeutic agents or treatment modality, suitable to be administered together, sequentially, or in alternation. Other compounds of Formulae (I)-(VIa) suitable for the methods of the disclosure are described in U.S. Publication 20120264734, the contents of which are hereby incorporated by reference in their entireties.

A compound (i.e., an EZH2 inhibitor) that can be used in any methods described herein may have the following Formula I:

or a pharmaceutically acceptable salt thereof; wherein

R⁷⁰¹ is H, F, OR⁷⁰⁷, NHR⁷⁰⁷, —(C≡C)—(CH₂)_(n7)—R⁷⁰⁸, phenyl, 5- or 6-membered heteroaryl, C₃₋₈ cycloalkyl, or 4-7 membered heterocycloalkyl containing 1-3 heteroatoms, wherein the phenyl, 5- or 6-membered heteroaryl, C₃₋₈ cycloalkyl or 4-7 membered heterocycloalkyl each independently is optionally substituted with one or more groups selected from halo, C₁₋₃ alkyl, OH, O—C₁₋₆ alkyl, NH—C₁₋₆ alkyl, and, C₁₋₃ alkyl substituted with C₃₋₈ cycloalkyl or 4-7 membered heterocycloalkyl containing 1-3 heteroatoms, wherein each of the O—C₁₋₆ alkyl and NH—C₁₋₆ alkyl is optionally substituted with hydroxyl, O—C₁₋₃ alkyl or NH—C₁₋₃ alkyl, each of the O—C₁₋₃ alkyl and NH—C₁₋₃ alkyl being optionally further substituted with O—C₁₋₃ alkyl or NH—C₁₋₃ alkyl;

each of R⁷⁰² and R⁷⁰³, independently is H, halo, C₁₋₄ alkyl, C₁₋₆ alkoxyl or C₆-C₁₀ aryloxy, each optionally substituted with one or more halo;

each of R⁷⁰⁴ and R⁷⁰⁵, independently is C₁₋₄ alkyl;

R⁷⁰⁶ is cyclohexyl substituted by N(C₁₋₄ alkyl)₂ wherein one or both of the C₁₋₄ alkyl is substituted with C₁₋₆ alkoxy; or R⁷⁰⁶ is tetrahydropyranyl;

R⁷⁰⁷ is C₁₋₄ alkyl optionally substituted with one or more groups selected from hydroxyl, C₁₋₄ alkoxy, amino, mono- or di-C₁₋₄ alkylamino, C₃₋₈ cycloalkyl, and 4-7 membered heterocycloalkyl containing 1-3 heteroatoms, wherein the C₃₋₈ cycloalkyl or 4-7 membered heterocycloalkyl each independently is further optionally substituted with C₁₋₃ alkyl;

R⁷⁰⁸ is C₁₋₄ alkyl optionally substituted with one or more groups selected from OH, halo, and C₁₋₄ alkoxy, 4-7 membered heterocycloalkyl containing 1-3 heteroatoms, or O—C₁₋₆ alkyl, wherein the 4-7 membered heterocycloalkyl can be optionally further substituted with OH or C₁₋₆ alkyl; and

n₇ is 0, 1 or 2.

For example, R⁷⁰⁶ is cyclohexyl substituted by N(C₁₋₄ alkyl)₂ wherein one of the C₁₋₄ alkyl is unsubstituted and the other is substituted with methoxy.

For example, R⁷⁰⁶ is

For example, the compound is of Formula II:

For example, R⁷⁰² is methyl or isopropyl and R⁷⁰³ is methyl or methoxyl.

For example, R⁷⁰⁴ is methyl.

For example, R⁷⁰¹ is OR⁷⁰⁷ and R⁷⁰⁷ is C₁₋₃ alkyl optionally substituted with OCH₃ or morpholine.

For example, R⁷⁰¹ is H or F.

For example, R⁷⁰¹ is tetrahydropyranyl, phenyl, pyridyl, pyrimidyl, pyrazinyl, imidazolyl, or pyrazolyl, each of which is optionally substituted with methyl, methoxy, ethyl substituted with morpholine, or —OCH₂CH₂OCH₃.

For example, R⁷⁰⁸ is morpholine, piperidine, piperazine, pyrrolidine, diazepane, or azetidine, each of which is optionally substituted with OH or C₁₋₆ alkyl.

For example, R⁷⁰⁸ is morpholine

For example, R⁷⁰⁸ is piperazine substituted with C₁₋₆ alkyl.

For example, R⁷⁰⁸ is methyl, t-butyl or C(CH₃)₂OH.

A compound (i.e., an EZH2 inhibitor) that can be used in any methods described herein may have the following Formula III:

or a pharmaceutically acceptable salt thereof.

In this formula:

R⁸⁰¹ is C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₈ cycloalkyl, 4-7 membered heterocycloalkyl containing 1-3 heteroatoms, phenyl or 5- or 6-membered heteroaryl, each of which is substituted with O—C₁₋₆ alkyl-R_(x) or NH—C₁₋₆ alkyl-R_(x), wherein R_(x) is hydroxyl, O—C₁₋₃ alkyl or NH—C₁₋₃ alkyl, and R_(x) is optionally further substituted with O—C₁₋₃ alkyl or NH—C₁₋₃ alkyl except when R_(x) is hydroxyl; or R⁸⁰¹ is phenyl substituted with -Q₂-T₂, wherein Q₂ is a bond or C₁-C₃ alkyl linker optionally substituted with halo, cyano, hydroxyl or C₁-C₆ alkoxy, and T₂ is optionally substituted 4- to 12-membered heterocycloalkyl; and R⁸⁰¹ is optionally further substituted;

each of R⁸⁰² and R⁸⁰³, independently is H, halo, C₁₋₄ alkyl, C₁₋₆ alkoxyl or C₆-C₁₀ aryloxy, each optionally substituted with one or more halo;

each of R⁸⁰⁴ and R⁸⁰⁵, independently is C₁₋₄ alkyl; and

R⁸⁰⁶ is -Q_(x)-T_(x), wherein Q_(x) is a bond or C₁₋₄ alkyl linker, T_(x) is H, optionally substituted C₁₋₄ alkyl, optionally substituted C₃-C₈ cycloalkyl or optionally substituted 4- to 14-membered heterocycloalkyl.

For example, each of Q_(x) and Q₂ independently is a bond or methyl linker, and each of T_(x) and T₂ independently is tetrahydropyranyl, piperidinyl substituted by 1, 2, or 3 C₁-4 alkyl groups, or cyclohexyl substituted by N(C₁₋₄ alkyl)₂ wherein one or both of the C₁₋₄ alkyl is optionally substituted with C₁₋₆ alkoxy;

For example, R⁸⁰⁶ is cyclohexyl substituted by N(C₁₋₄ alkyl)₂ or R⁸⁰⁶ is tetrahydropyranyl.

For example, R⁸⁰⁶ is

For example, R⁸⁰¹ is phenyl or 5- or 6-membered heteroaryl substituted with O—C₁₋₆ alkyl-R_(x), or R⁸⁰¹ is phenyl, substituted with CH₂-tetrahydropyranyl.

For example, a compound of the present disclosure is of Formula IVa or IVb:

wherein Z′ is CH or N, and R⁸⁰⁷ is C₂₋₃ alkyl-R_(x).

For example, R⁸⁰⁷ is —CH₂CH₂OH, —CH₂CH₂OCH₃, or —CH₂CH₂OCH₂CH₂OCH₃.

For example, R⁸⁰² is methyl or isopropyl and R⁸⁰³ is methyl or methoxyl.

For example, R⁸⁰⁴ is methyl.

A compound of the present disclosure may have the following Formula (V):

or a pharmaceutically acceptable salt or ester thereof.

In this formula:

R₂, R₄ and R₁₂ are each, independently C₁₋₆ alkyl;

R₆ is C₆-C₁₀ aryl or 5- or 6-membered heteroaryl, each of which is optionally substituted with one or more -Q₂-T₂, wherein Q₂ is a bond or C₁-C₃ alkyl linker optionally substituted with halo, cyano, hydroxyl or C₁-C₆ alkoxy, and T₂ is H, halo, cyano, —OR_(a), —NR_(a)R_(b), —(NR_(a)R_(b)R_(c))⁺A⁻, —C(O)R_(a), —C(O)OR_(a), —C(O)NR_(a)R_(b), —NR_(b)C(O)R_(a), —NR_(b)C(O)OR_(a), —S(O)₂R_(a), —S(O)₂NR_(a)R_(b), or R_(S2), in which each of R_(a), R_(b), and R_(e), independently is H or R_(S3), A⁻ is a pharmaceutically acceptable anion, each of R_(S2) and R_(S3), independently, is C₁-C₆ alkyl, C₃—C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or R_(a) and R_(b), together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of R_(S2), R_(S3), and the 4 to 12-membered heterocycloalkyl ring formed by R_(a) and R_(b), is optionally substituted with one or more -Q₃-T₃, wherein Q₃ is a bond or C₁-C₃ alkyl linker each optionally substituted with halo, cyano, hydroxyl or C₁-C₆ alkoxy, and T₃ is selected from the group consisting of halo, cyano, C₁-C₆ alkyl, C₃-C₅ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, OR_(d), COOR_(d), —S(O)₂R_(d), —NR_(d)R_(e), and —C(O)NR_(d)R_(e), each of R_(d) and R_(e) independently being H or C₁-C₆ alkyl, or -Q₃-T₃ is oxo; or any two neighboring -Q₂-T₂, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₅ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl;

R₇ is -Q₄-T₄, in which Q₄ is a bond, C₁-C₄ alkyl linker, or C₂-C₄ alkenyl linker, each linker optionally substituted with halo, cyano, hydroxyl or C₁-C₆ alkoxy, and T₄ is H, halo, cyano, NR_(f)R_(g), —OR_(f), —C(O)R_(f), —C(O)OR_(f), —C(O)NR_(f)R_(g), —C(O)NR_(f)OR_(g), —NR_(f)C(O)R_(g), —S(O)₂R_(f), or R_(S4), in which each of R_(f) and R_(g), independently is H or R_(S5), each of R_(S4) and R_(S5), independently is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, and each of R_(S4) and R_(S5) is optionally substituted with one or more -Q₅-T₅, wherein Q₅ is a bond, C(O), C(O)NR_(k), NR_(k)C(O), S(O)₂, or C₁-C₃ alkyl linker, R_(k) being H or C₁-C₆ alkyl, and T₅ is H, halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or S(O)_(q)R_(q) in which q is 0, 1, or 2 and R_(q) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₅ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, and T₅ is optionally substituted with one or more substituents selected from the group consisting of halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl except when T₅ is H, halo, hydroxyl, or cyano; or -Q₅-T₅ is oxo; and

R₈ is H, halo, hydroxyl, COOH, cyano, R_(S6), OR_(S6), or COOR_(S6), in which R_(S6) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈ cycloalkyl, 4 to 12-membered heterocycloalkyl, amino, mono-C₁-C₆ alkylamino, or di-C₁-C₆ alkylamino, and R_(S6) is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, and di-C₁-C₆ alkylamino; or R₇ and R₈, together with the N atom to which they are attached, form a 4 to 11-membered heterocycloalkyl ring having 0 to 2 additional heteroatoms, and the 4 to 11-membered heterocycloalkyl ring formed by R₇ and R₈ is optionally substituted with one or more -Q₆-T₆, wherein Q₆ is a bond, C(O), C(O)NR_(m), NR_(m)C(O), S(O)₂, or C₁-C₃ alkyl linker, R_(m) being H or C₁-C₆ alkyl, and T₆ is H, halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or S(O)_(p)R_(p) in which p is 0, 1, or 2 and R_(p) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₅ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, and T₆ is optionally substituted with one or more substituents selected from the group consisting of halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl except when T₆ is H, halo, hydroxyl, or cyano; or -Q₆-T₆ is oxo.

For example, R₆ is C₆-C₁₀ aryl or 5- or 6-membered heteroaryl, each of which is optionally, independently substituted with one or more -Q₂-T₂, wherein Q₂ is a bond or C₁-C₃ alkyl linker, and T₂ is H, halo, cyano, —OR_(a), —NR_(a)R_(b), —(NR_(a)R_(b)R_(c))⁺A⁻, —C(O)NR_(a)R_(b), —NR_(b)C(O)R_(a), —S(O)₂R_(a), or R_(S2), in which each of R_(a) and R_(b), independently is H or R_(S3), each of R_(S2) and R_(S3), independently, is C₁-C₆ alkyl, or R_(a) and R_(b), together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of R_(S2), R_(S3), and the 4 to 7-membered heterocycloalkyl ring formed by R_(a) and R_(b), is optionally, independently substituted with one or more -Q₃-T₃, wherein Q₃ is a bond or C₁-C₃ alkyl linker and T₃ is selected from the group consisting of halo, C₁-C₆ alkyl, 4 to 7-membered heterocycloalkyl, OR_(d), —S(O)₂R_(d), and —NR_(d)R_(e), each of R_(d) and R_(e) independently being H or C₁-C₆ alkyl, or -Q₃-T₃ is oxo; or any two neighboring -Q₂-T₂, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S.

For example, the compound of the present disclosure is of Formula (VI):

or a pharmaceutically acceptable salt thereof, wherein Q₂ is a bond or methyl linker, T₂ is H, halo, —OR_(a), —NR_(a)R_(b), —(NR_(a)R_(b)R_(c))⁺A⁻, or —S(O)₂NR_(a)R_(b), R₇ is piperidinyl, tetrahydropyran, cyclopentyl, or cyclohexyl, each optionally substituted with one -Q₅-T₅ and R₈ is ethyl.

The present disclosure provides the compounds of Formula (VIa):

or a pharmaceutically acceptable salts or esters thereof, wherein R₇, R₈, R_(a), and R_(b) are defined herein.

The compounds of Formula (VIa) can include one or more of the following features:

For example, each of R_(a) and R_(b) independently is H or C₁-C₆ alkyl optionally substituted with one or more -Q₃-T₃.

For example, one of R_(a) and R_(b) is H.

For example, R_(a) and R_(b), together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom (e.g., azetidinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, morpholinyl, 1,4-diazepanyl, 1,4-oxazepanyl, 2-oxa-5-azabicyclo[2.2.1]heptanyl, 2,5-diazabicyclo[2.2.1]heptanyl, and the like) and the ring is optionally substituted with one or more -Q₃-T₃.

For example, R_(a) and R_(b), together with the N atom to which they are attached, form azetidinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, or morpholinyl, and the ring is optionally substituted with one or more -Q₃-T₃.

For example, one or more -Q₃-T₃ are oxo.

For example, Q₃ is a bond or unsubstituted or substituted C₁-C₃ alkyl linker.

For example, T₃ is H, halo, 4 to 7-membered heterocycloalkyl, C₁-C₃ alkyl, OR_(d), COOR_(d), —S(O)₂R_(d), or —NR_(d)R_(e).

For example, each of R_(d) and R_(e) independently being H or C₁-C₆ alkyl.

For example, R₇ is C₃-C₈ cycloalkyl or 4 to 7-membered heterocycloalkyl, each optionally substituted with one or more -Q₅-T₅.

For example, R₇ is piperidinyl, tetrahydropyran, tetrahydro-2H-thiopyranyl, cyclopentyl, cyclohexyl, pyrrolidinyl, or cycloheptyl, each optionally substituted with one or more -Q₅-T₅.

For example, R₇ is cyclopentyl cyclohexyl or tetrahydro-2H-thiopyranyl, each of which is optionally substituted with one or more -Q₅-T₅.

For example, Q₅ is NHC(O) and T₅ is C₁-C₆ alkyl or C₁-C₆ alkoxy, each

For example, one or more -Q₅-T₅ are oxo.

For example, R₇ is 1-oxide-tetrahydro-2H-thiopyranyl or 1,1-dioxide-tetrahydro-2H-thiopyranyl.

For example, Q₅ is a bond and T₅ is amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino.

For example, Q₅ is CO, S(O)₂, or NHC(O); and T₅ is C₁-C₆ alkyl, C₁-C₆ alkoxyl, C₃-C₅ cycloalkyl, or 4 to 7-membered heterocycloalkyl.

For example, R₈ is H or C₁-C₆ alkyl which is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, and di-C₁-C₆ alkylamino.

For example, R₈ is H, methyl, or ethyl.

In one embodiment, the compound of the disclosure is Compound 44

or a pharmaceutically acceptable salt thereof.

In some embodiments, a compound that can be used in any methods presented here is:

stereoisomers thereof or pharmaceutically acceptable salts and solvates thereof.

In some embodiments, a compound that can be used in any methods presented here is GSK-126, stereoisomers thereof or pharmaceutically acceptable salts and solvates thereof.

In one embodiment, the compound of the disclosure is the compound itself, i.e., the free base or “naked” molecule. In another embodiment, the compound is a salt thereof, e.g., a mono-HCl or tri-HCl salt, mono-HBr or tri-HBr salt of the naked molecule.

Representative compounds of the present disclosure include compounds listed in Table 1.

In the table below, each occurrence of

should be construed as

TABLE 1 Compound MS Number Structure (M + 1)⁺ 1

501.39 2

543.22 3

486.21 4

529.30 11

558.45 12

559.35 13

517.3  14

557.4  16

515.4  20

614.4  21

614.4  27

516.35 36

557.35 39

572.35 40

572.35 42

572.4  43

572.6  44

573.40 47

530.35 59

587.40 60

601.30 61

599.35 62

601.35 63

613.35 65

531.30 66

586.40 67

585.25 68

585.35 69

557.25 70

573.40 71

573.40 72

575.35 73

572.10 74

575.35 75

571.25 76

587.40 77

587.45 78

587.20 79

589.35 80

589.30 81

607.35 82

543.40 83

559.80 84

561.25 85

86

585.37 87

600.30 88

587.40 89

503.40 90

517.30 91

531.35 92

545.40 93

557.35 94

559.20 95

599.35 (M + Na) 96

577.25 97

571.40 98

547.35 99

561.30 100

591.25 101

546.35 102

560.20 103

567.30 104

585.25 105

585.40 107

108

530.35 114

573.25 115

642.45 116

545.15 117

489.20 119

609.35 122

587.55 124

650.85 125

614.75 126

572.35 127

656.65 128

586.45 129

628.35 130

591.2  131

587.35 132

589.25 133

605.25 135

621.40 136

621.45 137

589.35 138

627.5  141

614.65 142

603.45 143

578.35 144

609.15 146

641.50 178

593.60

As used herein, “alkyl”, “C₁, C₂, C₃, C₄, C₅ or C₆ alkyl” or “C₁-C₆ alkyl” is intended to include C₁, C₂, C₃, C₄, C₅ or C₆ straight chain (linear) saturated aliphatic hydrocarbon groups and C₃, C₄, C₅ or C₆ branched saturated aliphatic hydrocarbon groups. For example, C₁-C₆ alkyl is intended to include C₁, C₂, C₃, C₄, C₅ and C₆ alkyl groups. Examples of alkyl include, moieties having from one to six carbon atoms, such as, but not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl or n-hexyl.

In certain embodiments, a straight chain or branched alkyl has six or fewer carbon atoms (e.g., C₁-C₆ for straight chain, C₃-C₆ for branched chain), and in another embodiment, a straight chain or branched alkyl has four or fewer carbon atoms.

As used herein, the term “cycloalkyl” refers to a saturated or unsaturated nonaromatic hydrocarbon mono- or multi-ring (e.g., fused, bridged, or spiro rings) system having 3 to 30 carbon atoms (e.g., C₃-C₁₀). Examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, and adamantyl. The term “heterocycloalkyl” refers to a saturated or unsaturated nonaromatic 3-8 membered monocyclic, 7-12 membered bicyclic (fused, bridged, or spiro rings), or 11-14 membered tricyclic ring system (fused, bridged, or spiro rings) having one or more heteroatoms (such as O, N, S, or Se), unless specified otherwise. Examples ofheterocycloalkyl groups include, but are not limited to, piperidinyl, piperazinyl, pyrrolidinyl, dioxanyl, tetrahydrofuranyl, isoindolinyl, indolinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, oxiranyl, azetidinyl, oxetanyl, thietanyl, 1,2,3,6-tetrahydropyridinyl, tetrahydropyranyl, dihydropyranyl, pyranyl, morpholinyl, 1,4-diazepanyl, 1,4-oxazepanyl, 2-oxa-5-azabicyclo[2.2.1]heptanyl, 2,5-diazabicyclo[2.2.1]heptanyl, 2-oxa-6-azaspiro[3.3]heptanyl, 2,6-diazaspiro[3.3]heptanyl, 1,4-dioxa-8-azaspiro[4.5]decanyl and the like.

The term “optionally substituted alkyl” refers to unsubstituted alkyl or alkyl having designated substituents replacing one or more hydrogen atoms on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

An “arylalkyl” or an “aralkyl” moiety is an alkyl substituted with an aryl (e.g., phenylmethyl (benzyl)). An “alkylaryl” moiety is an aryl substituted with an alkyl (e.g., methylphenyl).

As used herein, “alkyl linker” is intended to include C₁, C₂, C₃, C₄, C₅ or C₆ straight chain (linear) saturated divalent aliphatic hydrocarbon groups and C₃, C₄, C₅ or C₆ branched saturated aliphatic hydrocarbon groups. For example, C₁-C₆ alkyl linker is intended to include C₁, C₂, C₃, C₄, C₅ and C₆ alkyl linker groups. Examples of alkyl linker include, moieties having from one to six carbon atoms, such as, but not limited to, methyl (—CH₂—), ethyl (—CH₂CH₂—), n-propyl (—CH₂CH₂CH₂—), i-propyl (—CHCH3CH₂—), n-butyl (—CH₂CH₂CH₂CH₂—), s-butyl (—CHCH3CH₂CH₂—), i-butyl (—C(CH₃) 2CH₂—), n-pentyl (—CH₂CH₂CH₂CH₂CH₂—), s-pentyl (—CHCH3CH₂CH₂CH₂—) or n-hexyl (—CH₂CH₂CH₂CH₂CH₂CH₂—).

“Alkenyl” includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double bond. For example, the term “alkenyl” includes straight chain alkenyl groups (e.g., ethenyl, propenyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl), and branched alkenyl groups. In certain embodiments, a straight chain or branched alkenyl group has six or fewer carbon atoms in its backbone (e.g., C₂-C₆ for straight chain, C₃-C₆ for branched chain). The term “C₂-C₆” includes alkenyl groups containing two to six carbon atoms. The term “C₃-C₆” includes alkenyl groups containing three to six carbon atoms.

The term “optionally substituted alkenyl” refers to unsubstituted alkenyl or alkenyl having designated substituents replacing one or more hydrogen atoms on one or more hydrocarbon backbone carbon atoms. Such substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

“Alkynyl” includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but which contain at least one triple bond. For example, “alkynyl” includes straight chain alkynyl groups (e.g., ethynyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl), and branched alkynyl groups. In certain embodiments, a straight chain or branched alkynyl group has six or fewer carbon atoms in its backbone (e.g., C₂-C₆ for straight chain, C₃-C₆ for branched chain). The term “C₂-C₆” includes alkynyl groups containing two to six carbon atoms. The term “C₃-C₆” includes alkynyl groups containing three to six carbon atoms.

The term “optionally substituted alkynyl” refers to unsubstituted alkynyl or alkynyl having designated substituents replacing one or more hydrogen atoms on one or more hydrocarbon backbone carbon atoms. Such substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

Other optionally substituted moieties (such as optionally substituted cycloalkyl, heterocycloalkyl, aryl, or heteroaryl) include both the unsubstituted moieties and the moieties having one or more of the designated substituents. For example, substituted heterocycloalkyl includes those substituted with one or more alkyl groups, such as 2,2,6,6-tetramethyl-piperidinyl and 2,2,6,6-tetramethyl-1,2,3,6-tetrahydropyridinyl.

“Aryl” includes groups with aromaticity, including “conjugated,” or multicyclic systems with at least one aromatic ring and do not contain any heteroatom in the ring structure. Examples include phenyl, benzyl, 1,2,3,4-tetrahydronaphthalenyl, etc.

“Heteroaryl” groups are aryl groups, as defined above, except having from one to four heteroatoms in the ring structure, and may also be referred to as “aryl heterocycles” or “heteroaromatics.” As used herein, the term “heteroaryl” is intended to include a stable 5-, 6-, or 7-membered monocyclic or 7-, 8-, 9-, 10-, 11- or 12-membered bicyclic aromatic heterocyclic ring which consists of carbon atoms and one or more heteroatoms, e.g., 1 or 1-2 or 1-3 or 1-4 or 1-5 or 1-6 heteroatoms, or e.g. 1, 2, 3, 4, 5, or 6 heteroatoms, independently selected from the group consisting of nitrogen, oxygen and sulfur. The nitrogen atom may be substituted or unsubstituted (i.e., N or NR wherein R is H or other substituents, as defined). The nitrogen and sulfur heteroatoms may optionally be oxidized (i.e., N→O and S(O)_(p), where p=1 or 2). It is to be noted that total number of S and O atoms in the aromatic heterocycle is not more than 1.

Examples of heteroaryl groups include pyrrole, furan, thiophene, thiazole, isothiazole, imidazole, triazole, tetrazole, pyrazole, oxazole, isoxazole, pyridine, pyrazine, pyridazine, pyrimidine, and the like.

Furthermore, the terms “aryl” and “heteroaryl” include multicyclic aryl and heteroaryl groups, e.g., tricyclic, bicyclic, e.g., naphthalene, benzoxazole, benzodioxazole, benzothiazole, benzoimidazole, benzothiophene, methylenedioxyphenyl, quinoline, isoquinoline, naphthrydine, indole, benzofuran, purine, benzofuran, deazapurine, indolizine.

In the case of multicyclic aromatic rings, only one of the rings needs to be aromatic (e.g., 2,3-dihydroindole), although all of the rings may be aromatic (e.g., quinoline). The second ring can also be fused or bridged.

The cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring can be substituted at one or more ring positions (e.g., the ring-forming carbon or heteroatom such as N) with such substituents as described above, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkoxy, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, alkylaminocarbonyl, aralkylaminocarbonyl, alkenylaminocarbonyl, alkylcarbonyl, arylcarbonyl, aralkylcarbonyl, alkenylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylthiocarbonyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety. Aryl and heteroaryl groups can also be fused or bridged with alicyclic or heterocyclic rings, which are not aromatic so as to form a multicyclic system (e.g., tetralin, methylenedioxyphenyl).

As used herein, “carbocycle” or “carbocyclic ring” is intended to include any stable monocyclic, bicyclic or tricyclic ring having the specified number of carbons, any of which may be saturated, unsaturated, or aromatic. Carbocycle includes cycloalkyl and aryl. For example, a C₃-C₁₄ carbocycle is intended to include a monocyclic, bicyclic or tricyclic ring having 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 carbon atoms. Examples of carbocycles include, but are not limited to, cyclopropyl, cyclobutyl, cyclobutenyl, cyclopentyl, cyclopentenyl, cyclohexyl, cycloheptenyl, cycloheptyl, cycloheptenyl, adamantyl, cyclooctyl, cyclooctenyl, cyclooctadienyl, fluorenyl, phenyl, naphthyl, indanyl, adamantyl and tetrahydronaphthyl. Bridged rings are also included in the definition of carbocycle, including, for example, [3.3.0]bicyclooctane, [4.3.0]bicyclononane, [4.4.0]bicyclodecane and [2.2.2]bicyclooctane. A bridged ring occurs when one or more carbon atoms link two non-adjacent carbon atoms. In one embodiment, bridge rings are one or two carbon atoms. It is noted that a bridge always converts a monocyclic ring into a tricyclic ring. When a ring is bridged, the substituents recited for the ring may also be present on the bridge. Fused (e.g., naphthyl, tetrahydronaphthyl) and spiro rings are also included.

As used herein, “heterocycle” or “heterocyclic group” includes any ring structure (saturated, unsaturated, or aromatic) which contains at least one ring heteroatom (e.g., N, O or S). Heterocycle includes heterocycloalkyl and heteroaryl. Examples of heterocycles include, but are not limited to, morpholine, pyrrolidine, tetrahydrothiophene, piperidine, piperazine, oxetane, pyran, tetrahydropyran, azetidine, and tetrahydrofuran.

Examples of heterocyclic groups include, but are not limited to, acridinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzothiophenyl, benzoxazolyl, benzoxazolinyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazolinyl, carbazolyl, 4aH-carbazolyl, carbolinyl, chromanyl, chromenyl, cinnolinyl, decahydroquinolinyl, 2H,6H-1,5,2-dithiazinyl, dihydrofuro[2,3-b]tetrahydrofuran, furanyl, furazanyl, imidazolidinyl, imidazolinyl, imidazolyl, 1H-indazolyl, indolenyl, indolinyl, indolizinyl, indolyl, 3H-indolyl, isatinoyl, isobenzofuranyl, isochromanyl, isoindazolyl, isoindolinyl, isoindolyl, isoquinolinyl, isothiazolyl, isoxazolyl, methylenedioxyphenyl, morpholinyl, naphthyridinyl, octahydroisoquinolinyl, oxadiazolyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl, 1,2,4-oxadiazol5(4H)-one, oxazolidinyl, oxazolyl, oxindolyl, pyrimidinyl, phenanthridinyl, phenanthrolinyl, phenazinyl, phenothiazinyl, phenoxathinyl, phenoxazinyl, phthalazinyl, piperazinyl, piperidinyl, piperidonyl, 4-piperidonyl, piperonyl, pteridinyl, purinyl, pyranyl, pyrazinyl, pyrazolidinyl, pyrazolinyl, pyrazolyl, pyridazinyl, pyridooxazole, pyridoimidazole, pyridothiazole, pyridinyl, pyridyl, pyrimidinyl, pyrrolidinyl, pyrrolinyl, 2H-pyrrolyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, quinuclidinyl, tetrahydrofuranyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, tetrazolyl, 6H-1,2,5-thiadiazinyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thianthrenyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, thiophenyl, triazinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, 1,3,4-triazolyl and xanthenyl.

The term “substituted,” as used herein, means that any one or more hydrogen atoms on the designated atom is replaced with a selection from the indicated groups, provided that the designated atom's normal valency is not exceeded, and that the substitution results in a stable compound. When a substituent is oxo or keto (i.e., ═O), then 2 hydrogen atoms on the atom are replaced. Keto substituents are not present on aromatic moieties. Ring double bonds, as used herein, are double bonds that are formed between two adjacent ring atoms (e.g., C═C, C═N or N═N). “Stable compound” and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.

When a bond to a substituent is shown to cross a bond connecting two atoms in a ring, then such substituent may be bonded to any atom in the ring. When a substituent is listed without indicating the atom via which such substituent is bonded to the rest of the compound of a given formula, then such substituent may be bonded via any atom in such formula. Combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds.

When any variable (e.g., R₁) occurs more than one time in any constituent or formula for a compound, its definition at each occurrence is independent of its definition at every other occurrence. Thus, for example, if a group is shown to be substituted with 0-2 R₁ moieties, then the group may optionally be substituted with up to two R₁ moieties and R₁ at each occurrence is selected independently from the definition of R₁. Also, combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds.

The term “hydroxy” or “hydroxyl” includes groups with an —OH or —O—.

As used herein, “halo” or “halogen” refers to fluoro, chloro, bromo and iodo. The term “perhalogenated” generally refers to a moiety wherein all hydrogen atoms are replaced by halogen atoms. The term “haloalkyl” or “haloalkoxyl” refers to an alkyl or alkoxyl substituted with one or more halogen atoms.

The term “carbonyl” includes compounds and moieties which contain a carbon connected with a double bond to an oxygen atom. Examples of moieties containing a carbonyl include, but are not limited to, aldehydes, ketones, carboxylic acids, amides, esters, anhydrides, etc.

The term “carboxyl” refers to —COOH or its C₁-C₆ alkyl ester.

“Acyl” includes moieties that contain the acyl radical (R—C(O)—) or a carbonyl group. “Substituted acyl” includes acyl groups where one or more of the hydrogen atoms are replaced by, for example, alkyl groups, alkynyl groups, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

“Aroyl” includes moieties with an aryl or heteroaromatic moiety bound to a carbonyl group. Examples of aroyl groups include phenylcarboxy, naphthyl carboxy, etc.

“Alkoxyalkyl,” “alkylaminoalkyl,” and “thioalkoxyalkyl” include alkyl groups, as described above, wherein oxygen, nitrogen, or sulfur atoms replace one or more hydrocarbon backbone carbon atoms.

The term “alkoxy” or “alkoxyl” includes substituted and unsubstituted alkyl, alkenyl and alkynyl groups covalently linked to an oxygen atom. Examples of alkoxy groups or alkoxyl radicals include, but are not limited to, methoxy, ethoxy, isopropyloxy, propoxy, butoxy and pentoxy groups. Examples of substituted alkoxy groups include halogenated alkoxy groups. The alkoxy groups can be substituted with groups such as alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moieties. Examples of halogen substituted alkoxy groups include, but are not limited to, fluoromethoxy, difluoromethoxy, trifluoromethoxy, chloromethoxy, dichloromethoxy and trichloromethoxy.

The term “ether” or “alkoxy” includes compounds or moieties which contain an oxygen bonded to two carbon atoms or heteroatoms. For example, the term includes “alkoxyalkyl,” which refers to an alkyl, alkenyl, or alkynyl group covalently bonded to an oxygen atom which is covalently bonded to an alkyl group.

The term “ester” includes compounds or moieties which contain a carbon or a heteroatom bound to an oxygen atom which is bonded to the carbon of a carbonyl group. The term “ester” includes alkoxycarboxy groups such as methoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl, pentoxycarbonyl, etc.

The term “thioalkyl” includes compounds or moieties which contain an alkyl group connected with a sulfur atom. The thioalkyl groups can be substituted with groups such as alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, carboxyacid, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moieties.

The term “thiocarbonyl” or “thiocarboxy” includes compounds and moieties which contain a carbon connected with a double bond to a sulfur atom.

The term “thioether” includes moieties which contain a sulfur atom bonded to two carbon atoms or heteroatoms. Examples of thioethers include, but are not limited to alkthioalkyls, alkthioalkenyls, and alkthioalkynyls. The term “alkthioalkyls” include moieties with an alkyl, alkenyl, or alkynyl group bonded to a sulfur atom which is bonded to an alkyl group. Similarly, the term “alkthioalkenyls” refers to moieties wherein an alkyl, alkenyl or alkynyl group is bonded to a sulfur atom which is covalently bonded to an alkenyl group; and alkthioalkynyls” refers to moieties wherein an alkyl, alkenyl or alkynyl group is bonded to a sulfur atom which is covalently bonded to an alkynyl group.

As used herein, “amine” or “amino” refers to unsubstituted or substituted —NH₂. “Alkylamino” includes groups of compounds wherein nitrogen of —NH₂ is bound to at least one alkyl group. Examples of alkylamino groups include benzylamino, methylamino, ethylamino, phenethylamino, etc. “Dialkylamino” includes groups wherein the nitrogen of —NH₂ is bound to at least two additional alkyl groups. Examples of dialkylamino groups include, but are not limited to, dimethylamino and diethylamino. “Arylamino” and “diarylamino” include groups wherein the nitrogen is bound to at least one or two aryl groups, respectively. “Aminoaryl” and “aminoaryloxy” refer to aryl and aryloxy substituted with amino. “Alkylarylamino,” “alkylaminoaryl” or “arylaminoalkyl” refers to an amino group which is bound to at least one alkyl group and at least one aryl group. “Alkaminoalkyl” refers to an alkyl, alkenyl, or alkynyl group bound to a nitrogen atom which is also bound to an alkyl group. “Acylamino” includes groups wherein nitrogen is bound to an acyl group. Examples of acylamino include, but are not limited to, alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido groups.

The term “amide” or “aminocarboxy” includes compounds or moieties that contain a nitrogen atom that is bound to the carbon of a carbonyl or a thiocarbonyl group. The term includes “alkaminocarboxy” groups that include alkyl, alkenyl or alkynyl groups bound to an amino group which is bound to the carbon of a carbonyl or thiocarbonyl group. It also includes “arylaminocarboxy” groups that include aryl or heteroaryl moieties bound to an amino group that is bound to the carbon of a carbonyl or thiocarbonyl group. The terms “alkylaminocarboxy”, “alkenylaminocarboxy”, “alkynylaminocarboxy” and “arylaminocarboxy” include moieties wherein alkyl, alkenyl, alkynyl and aryl moieties, respectively, are bound to a nitrogen atom which is in turn bound to the carbon of a carbonyl group. Amides can be substituted with substituents such as straight chain alkyl, branched alkyl, cycloalkyl, aryl, heteroaryl or heterocycle. Substituents on amide groups may be further substituted.

Compounds of the present disclosure that contain nitrogens can be converted to N-oxides by treatment with an oxidizing agent (e.g., 3-chloroperoxybenzoic acid (mCPBA) and/or hydrogen peroxides) to afford other compounds of the present disclosure. Thus, all shown and claimed nitrogen-containing compounds are considered, when allowed by valency and structure, to include both the compound as shown and its N-oxide derivative (which can be designated as N→O or N⁺—O⁻). Furthermore, in other instances, the nitrogens in the compounds of the present disclosure can be converted to N-hydroxy or N-alkoxy compounds. For example, N-hydroxy compounds can be prepared by oxidation of the parent amine by an oxidizing agent such as m-CPBA. All shown and claimed nitrogen-containing compounds are also considered, when allowed by valency and structure, to cover both the compound as shown and its N-hydroxy (i.e., N—OH) and N-alkoxy (i.e., N—OR, wherein R is substituted or unsubstituted C₁-C₆ alkyl, C₁-C₆ alkenyl, C₁-C₆ alkynyl, 3-14-membered carbocycle or 3-14-membered heterocycle) derivatives.

“Isomerism” means compounds that have identical molecular formulae but differ in the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.” Stereoisomers that are not mirror images of one another are termed “diastereoisomers,” and stereoisomers that are non-superimposable mirror images of each other are termed “enantiomers” or sometimes optical isomers. A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a “racemic mixture.”

A carbon atom bonded to four nonidentical substituents is termed a “chiral center.”

“Chiral isomer” means a compound with at least one chiral center. Compounds with more than one chiral center may exist either as an individual diastereomer or as a mixture of diastereomers, termed “diastereomeric mixture.” When one chiral center is present, a stereoisomer may be characterized by the absolute configuration (R or S) of that chiral center. Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. The substituents attached to the chiral center under consideration are ranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog. (Cahn et al., Angew. Chem. Inter. Edit. 1966, 5, 385; errata 511; Cahn et al., Angew. Chem. 1966, 78, 413; Cahn and Ingold, J. Chem. Soc. 1951 (London), 612; Cahn et al., Experientia 1956, 12, 81; Cahn, J. Chem. Educ. 1964, 41, 116).

“Geometric isomer” means the diastereomers that owe their existence to hindered rotation about double bonds or a cycloalkyl linker (e.g., 1,3-cylcobutyl). These configurations are differentiated in their names by the prefixes cis and trans, or Z and E, which indicate that the groups are on the same or opposite side of the double bond in the molecule according to the Cahn-Ingold-Prelog rules.

It is to be understood that the compounds of the present disclosure may be depicted as different chiral isomers or geometric isomers. It should also be understood that when compounds have chiral isomeric or geometric isomeric forms, all isomeric forms are intended to be included in the scope of the present disclosure, and the naming of the compounds does not exclude any isomeric forms.

Furthermore, the structures and other compounds discussed in this disclosure include all atropic isomers thereof. “Atropic isomers” are a type of stereoisomer in which the atoms of two isomers are arranged differently in space. Atropic isomers owe their existence to a restricted rotation caused by hindrance of rotation of large groups about a central bond. Such atropic isomers typically exist as a mixture, however as a result of recent advances in chromatography techniques, it has been possible to separate mixtures of two atropic isomers in select cases.

“Tautomer” is one of two or more structural isomers that exist in equilibrium and is readily converted from one isomeric form to another. This conversion results in the formal migration of a hydrogen atom accompanied by a switch of adjacent conjugated double bonds. Tautomers exist as a mixture of a tautomeric set in solution. In solutions where tautomerization is possible, a chemical equilibrium of the tautomers will be reached. The exact ratio of the tautomers depends on several factors, including temperature, solvent and pH. The concept of tautomers that are interconvertable by tautomerizations is called tautomerism.

Of the various types of tautomerism that are possible, two are commonly observed. In keto-enol tautomerism a simultaneous shift of electrons and a hydrogen atom occurs. Ring-chain tautomerism arises as a result of the aldehyde group (—CHO) in a sugar chain molecule reacting with one of the hydroxy groups (—OH) in the same molecule to give it a cyclic (ring-shaped) form as exhibited by glucose.

Common tautomeric pairs are: ketone-enol, amide-nitrile, lactam-lactim, amide-imidic acid tautomerism in heterocyclic rings (e.g., in nucleobases such as guanine, thymine and cytosine), imine-enamine and enamine-enamine. An example of keto-enol equilibria is between pyridin-2(1H)-ones and the corresponding pyridin-2-ols, as shown below.

It is to be understood that the compounds of the present disclosure may be depicted as different tautomers. It should also be understood that when compounds have tautomeric forms, all tautomeric forms are intended to be included in the scope of the present disclosure, and the naming of the compounds does not exclude any tautomer form.

The compounds of Formulae (I)-(VIa) disclosed herein include the compounds themselves, as well as their salts and their solvates, if applicable. A salt, for example, can be formed between an anion and a positively charged group (e.g., amino) on an aryl- or heteroaryl-substituted benzene compound. Suitable anions include chloride, bromide, iodide, sulfate, bisulfate, sulfamate, nitrate, phosphate, citrate, methanesulfonate, trifluoroacetate, glutamate, glucuronate, glutarate, malate, maleate, succinate, fumarate, tartrate, tosylate, salicylate, lactate, naphthalenesulfonate, and acetate (e.g., trifluoroacetate). The term “pharmaceutically acceptable anion” refers to an anion suitable for forming a pharmaceutically acceptable salt. Likewise, a salt can also be formed between a cation and a negatively charged group (e.g., carboxylate) on an aryl- or heteroaryl-substituted benzene compound. Suitable cations include sodium ion, potassium ion, magnesium ion, calcium ion, and an ammonium cation such as tetramethylammonium ion. The aryl- or heteroaryl-substituted benzene compounds also include those salts containing quaternary nitrogen atoms. In the salt form, it is understood that the ratio of the compound to the cation or anion of the salt can be 1:1, or any ration other than 1:1, e.g., 3:1, 2:1, 1:2, or 1:3.

Additionally, the compounds of the present disclosure, for example, the salts of the compounds, can exist in either hydrated or unhydrated (the anhydrous) form or as solvates with other solvent molecules. Nonlimiting examples of hydrates include monohydrates, dihydrates, etc. Nonlimiting examples of solvates include ethanol solvates, acetone solvates, etc.

“Solvate” means solvent addition forms that contain either stoichiometric or non stoichiometric amounts of solvent. Some compounds have a tendency to trap a fixed molar ratio of solvent molecules in the crystalline solid state, thus forming a solvate. If the solvent is water the solvate formed is a hydrate; and if the solvent is alcohol, the solvate formed is an alcoholate. Hydrates are formed by the combination of one or more molecules of water with one molecule of the substance in which the water retains its molecular state as H₂O.

As used herein, the term “analog” refers to a chemical compound that is structurally similar to another but differs slightly in composition (as in the replacement of one atom by an atom of a different element or in the presence of a particular functional group, or the replacement of one functional group by another functional group). Thus, an analog is a compound that is similar or comparable in function and appearance, but not in structure or origin to the reference compound.

As defined herein, the term “derivative” refers to compounds that have a common core structure, and are substituted with various groups as described herein. For example, all of the compounds represented by Formula (I) are aryl- or heteroaryl-substituted benzene compounds, and have Formula (I) as a common core.

The term “bioisostere” refers to a compound resulting from the exchange of an atom or of a group of atoms with another, broadly similar, atom or group of atoms. The objective of a bioisosteric replacement is to create a new compound with similar biological properties to the parent compound. The bioisosteric replacement may be physicochemically or topologically based. Examples of carboxylic acid bioisosteres include, but are not limited to, acyl sulfonimides, tetrazoles, sulfonates and phosphonates. See, e.g., Patani and LaVoie, Chem. Rev. 96, 3147-3176, 1996.

The present disclosure is intended to include all isotopes of atoms occurring in the present compounds. Isotopes include those atoms having the same atomic number but different mass numbers. By way of general example and without limitation, isotopes of hydrogen include tritium and deuterium, and isotopes of carbon include C-13 and C-14.

Any compound of Formulae (I)-(VIa) of the present disclosure, as described herein, may be an EZH2 inhibitor.

In certain aspects of the disclosure an inhibitor of EZH2 “selectively inhibits” histone methyltransferase activity of the mutant EZH2 when it inhibits histone methyltransferase activity of the mutant EZH2 more effectively than it inhibits histone methyltransferase activity of wild-type EZH2. For example, in one embodiment the selective inhibitor has an IC50 for the mutant EZH2 that is at least 40 percent lower than the IC50 for wild-type EZH2. In one embodiment the selective inhibitor has an IC50 for the mutant EZH2 that is at least 50 percent lower than the IC50 for wild-type EZH2. In one embodiment the selective inhibitor has an IC50 for the mutant EZH2 that is at least 60 percent lower than the IC50 for wild-type EZH2. In one embodiment the selective inhibitor has an IC50 for the mutant EZH2 that is at least 70 percent lower than the IC50 for wild-type EZH2. In one embodiment the selective inhibitor has an IC50 for the mutant EZH2 that is at least 80 percent lower than the IC50 for wild-type EZH2. In one embodiment the selective inhibitor has an IC50 for the mutant EZH2 that is at least 90 percent lower than the IC50 for wild-type EZH2.

In one embodiment, the selective inhibitor of a mutant EZH2 exerts essentially no inhibitory effect on wild-type EZH2.

In certain aspects of the disclosure the inhibitor inhibits conversion of H3-K27me2 to H3-K27me3. In one embodiment the inhibitor is said to inhibit trimethylation of H3-K27. Since conversion of H3-K27me1 to H3-K27me2 precedes conversion of H3-K27me2 to H3-K27me3, an inhibitor of conversion of H3-K27me1 to H3-K27me2 naturally also inhibits conversion of H3-K27me2 to H3-K27me3, i.e., it inhibits trimethylation of H3-K27. It is also possible to inhibit conversion of H3-K27me2 to H3-K27me3 without inhibition of conversion of H3-K27me1 to H3-K27me2. Inhibition of this type would also result in inhibition of trimethylation of H3-K27, albeit without inhibition of dimethylation of H3-K27.

In one embodiment the inhibitor inhibits conversion of H3-K27me1 to H3-K27me2 and the conversion of H3-K27me2 to H3-K27me3. Such inhibitor may directly inhibit the conversion of H3-K27me1 to H3-K27me2 alone. Alternatively, such inhibitor may directly inhibit both the conversion of H3-K27me1 to H3-K27me2 and the conversion of H3-K27me2 to H3-K27me3.

In certain aspects of the disclosure, the inhibitor compound inhibits histone methyltransferase activity. Inhibition of histone methyltransferase activity can be detected using any suitable method. The inhibition can be measured, for example, either in terms of rate of histone methyltransferase activity or as product of histone methyltransferase activity.

The inhibition is a measurable inhibition compared to a suitable control. In one embodiment, inhibition is at least 10 percent inhibition compared to a suitable control. That is, the rate of enzymatic activity or the amount of product with the inhibitor is less than or equal to 90 percent of the corresponding rate or amount made without the inhibitor. In various other embodiments, inhibition is at least 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, or 95 percent inhibition compared to a suitable control. In one embodiment, inhibition is at least 99 percent inhibition compared to a suitable control. That is, the rate of enzymatic activity or the amount of product with the inhibitor is less than or equal to 1 percent of the corresponding rate or amount made without the inhibitor.

A composition of the present disclosure comprises a compound of Formulae (I)-(VIa), or a pharmaceutically acceptable salt thereof, and one or more other therapeutic agents, or a pharmaceutically acceptable salt thereof. The present disclosure provides for the administration of a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and one or more therapeutic agents or a pharmaceutically acceptable salt thereof, as a co-formulation or separate formulations, wherein the administration of formulations is simultaneous, sequential, or in alternation. In certain embodiments, the other therapeutic agents can be an agent that is recognized in the art as being useful to treat the disease or condition being treated by the composition of the present disclosure. In other embodiment, the other therapeutic agent can be an agent that is not recognized in the art as being useful to treat the disease or condition being treated by the composition of the present disclosure. In one aspect, the other therapeutic agents can be an agent that imparts a beneficial attribute to the composition of the present disclosure (e.g., an agent that affects the viscosity of the composition). The beneficial attribute to the composition of the present disclosure includes, but is not limited to, pharmacokinetic or pharmacodynamic co-action resulting from the combination of a compound of Formulae (I)-(VIa) and one or more other therapeutic agents. For example, the one or more other therapeutic agents can be anticancer agents or chemotherapeutic agents. For example, the one or more other therapeutic agents can be glucocorticoids. For example, the one or more other therapeutic agents can be selected from prednisone, prednisolone, cyclophosphamide, vincristine, doxorubicin, mafosfamide, cisplatin, AraC, everolimus, decitabine, dexamethasone, or functional analogs, derivatives, produgs, and metabolites thereof. In another aspect, the other therapeutic agent can be Prednisone or its active metabolite, Prednisolone.

The therapeutic agents set forth below are for illustrative purposes and not intended to be limiting. The present disclosure includes at least one other therapeutic agent selected from the lists below. The present disclosure can include more than one other therapeutic agent, e.g., two, three, four, or five other therapeutic agents such that the composition of the present disclosure can perform its intended function.

In one embodiment, the other therapeutic agent is an anticancer agent. In one embodiment, the anticancer agent is a compound that affects histone modifications, such as an HDAC inhibitor. In certain embodiments, an anticancer agent is selected from the group consisting of chemotherapeutics (such as 2CdA, 5-FU, 6-Mercaptopurine, 6-TG, Abraxane™, Accutane®, Actinomycin-D, Adriamycin®, Alimta®, all-trans retinoic acid, amethopterin, Ara-C, Azacitadine, BCNU, Blenoxane®, Camptosar®, CeeNU®, Clofarabine, Clolar™, Cytoxan®, daunorubicin hydrochloride, DaunoXome®, Dacogen®, DIC, Doxil®, Ellence®, Eloxatin®, Emcyt®, etoposide phosphate, Fludara®, FUDR®, Gemzar®, Gleevec®, hexamethylmelamine, Hycamtin®, Hydrea®, Idamycin®, Ifex®, ixabepilone, Ixempra®, L-asparaginase, Leukeran®, liposomal Ara-C, L-PAM, Lysodren, Matulane®, mithracin, Mitomycin-C, Myleran®, Navelbine®, Neutrexin®, nilotinib, Nipent®, Nitrogen Mustard, Novantrone®, Oncaspar®, Panretin®, Paraplatin®, Platinol®, prolifeprospan 20 with carmustine implant, Sandostatin®, Targretin®, Tasigna®, Taxotere®, Temodar®, TESPA, Trisenox®, Valstar®, Velban®, Vidaza™, vincristine sulfate, VM 26, Xeloda® and Zanosar®); biologics (such as Alpha Interferon, Bacillus Calmette-Guerin, Bexxar®, Campath®, Ergamisol®, Erlotinib, Herceptin®, Interleukin-2, Iressa®, lenalidomide, Mylotarg®, Ontak®, Pegasys®, Revlimid®, Rituxan®, Tarceva™ Thalomid®, Tykerb®, Velcade® and Zevalin™); corticosteroids, (such as dexamethasone sodium phosphate, DeltaSone® and Delta-Cortef®); hormonal therapies (such as Arimidex®, Aromasin®, Casodex®, Cytadren®, Eligard®, Eulexin®, Evista®, Faslodex®, Femara®, Halotestin®, Megace®, Nilandron®, Nolvadex®, Plenaxis™ and Zoladex®); and radiopharmaceuticals (such as Iodotope®, Metastron®, Phosphocol® and Samarium SM-153).

In another embodiment, the other therapeutic agent is a chemotherapeutic agent (also referred to as an anti-neoplastic agent or anti-proliferative agent), selected from the group including an alkylating agent; an antibiotic; an anti-metabolite; a detoxifying agent; an interferon; a polyclonal or monoclonal antibody; an EGFR inhibitor; a HER2 inhibitor; a histone deacetylase inhibitor; a hormone; a mitotic inhibitor; an MTOR inhibitor; a multi-kinase inhibitor; a serine/threonine kinase inhibitor; a tyrosine kinase inhibitors; a VEGF/VEGFR inhibitor; a taxane or taxane derivative, an aromatase inhibitor, an anthracycline, a microtubule targeting drug, a topoisomerase poison drug, an inhibitor of a molecular target or enzyme (e.g., a kinase or a protein methyltransferase), a cytidine analogue drug or any chemotherapeutic, anti-neoplastic or anti-proliferative agent listed in www.cancer.org/docroot/cdg/cdg_0.asp.

Exemplary alkylating agents include, but are not limited to, cyclophosphamide (Cytoxan; Neosar); chlorambucil (Leukeran); melphalan (Alkeran); carmustine (BiCNU); busulfan (Busulfex); lomustine (CeeNU); dacarbazine (DTIC-Dome); oxaliplatin (Eloxatin); carmustine (Gliadel); ifosfamide (Ifex); mechlorethamine (Mustargen); busulfan (Myleran); carboplatin (Paraplatin); cisplatin (CDDP; Platinol); temozolomide (Temodar); thiotepa (Thioplex); bendamustine (Treanda); or streptozocin (Zanosar).

Exemplary antibiotics include, but are not limited to, doxorubicin (Adriamycin); doxorubicin liposomal (Doxil); mitoxantrone (Novantrone); bleomycin (Blenoxane); daunorubicin (Cerubidine); daunorubicin liposomal (DaunoXome); dactinomycin (Cosmegen); epirubicin (Ellence); idarubicin (Idamycin); plicamycin (Mithracin); mitomycin (Mutamycin); pentostatin (Nipent); or valrubicin (Valstar).

Exemplary anti-metabolites include, but are not limited to, fluorouracil (Adrucil); capecitabine (Xeloda); hydroxyurea (Hydrea); mercaptopurine (Purinethol); pemetrexed (Alimta); fludarabine (Fludara); nelarabine (Arranon); cladribine (Cladribine Novaplus); clofarabine (Clolar); cytarabine (Cytosar-U); decitabine (Dacogen); cytarabine liposomal (DepoCyt); hydroxyurea (Droxia); pralatrexate (Folotyn); floxuridine (FUDR); gemcitabine (Gemzar); cladribine (Leustatin); fludarabine (Oforta); methotrexate (MTX; Rheumatrex); methotrexate (Trexall); thioguanine (Tabloid); TS-1 or cytarabine (Tarabine PFS).

Exemplary detoxifying agents include, but are not limited to, amifostine (Ethyol) or mesna (Mesnex).

Exemplary interferons include, but are not limited to, interferon alfa-2b (Intron A) or interferon alfa-2a (Roferon-A).

Exemplary polyclonal or monoclonal antibodies include, but are not limited to, trastuzumab (Herceptin); ofatumumab (Arzerra); bevacizumab (Avastin); rituximab (Rituxan); cetuximab (Erbitux); panitumumab (Vectibix); tositumomab/iodinel 31 tositumomab (Bexxar); alemtuzumab (Campath); ibritumomab (Zevalin; In-111; Y-90 Zevalin); gemtuzumab (Mylotarg); eculizumab (Soliris) ordenosumab.

Exemplary EGFR inhibitors include, but are not limited to, gefitinib (Iressa); lapatinib (Tykerb); cetuximab (Erbitux); erlotinib (Tarceva); panitumumab (Vectibix); PKI-166; canertinib (CI-1033); matuzumab (Emd7200) or EKB-569.

Exemplary HER2 inhibitors include, but are not limited to, trastuzumab (Herceptin); lapatinib (Tykerb) or AC-480.

Histone Deacetylase Inhibitors include, but are not limited to, vorinostat (Zolinza).

Exemplary hormones include, but are not limited to, tamoxifen (Soltamox; Nolvadex); raloxifene (Evista); megestrol (Megace); leuprolide (Lupron; Lupron Depot; Eligard; Viadur); fulvestrant (Faslodex); letrozole (Femara); triptorelin (Trelstar LA; Trelstar Depot); exemestane (Aromasin); goserelin (Zoladex); bicalutamide (Casodex); anastrozole (Arimidex); fluoxymesterone (Androxy; Halotestin); medroxyprogesterone (Provera; Depo-Provera); estramustine (Emcyt); flutamide (Eulexin); toremifene (Fareston); degarelix (Firmagon); nilutamide (Nilandron); abarelix (Plenaxis); or testolactone (Teslac).

Exemplary mitotic inhibitors include, but are not limited to, paclitaxel (Taxol; Onxol; Abraxane); docetaxel (Taxotere); vincristine (Oncovin; Vincasar PFS); vinblastine (Velban); etoposide (Toposar; Etopophos; VePesid); teniposide (Vumon); ixabepilone (Ixempra); nocodazole; epothilone; vinorelbine (Navelbine); camptothecin (CPT); irinotecan (Camptosar); topotecan (Hycamtin); amsacrine or lamellarin D (LAM-D).

Exemplary MTOR inhibitors include, but are not limited to, everolimus (Afinitor) or temsirolimus (Torisel); rapamune, ridaforolimus; or AP23573.

Exemplary VEGF/VEGFR inhibitors include, but are not limited to, bevacizumab (Avastin); sorafenib (Nexavar); sunitinib (Sutent); ranibizumab; pegaptanib; or vandetinib.

Exemplary microtubule targeting drugs include, but are not limited to, paclitaxel, docetaxel, vincristine, vinblastin, nocodazole, epothilones and navelbine.

Exemplary topoisomerase poison drugs include, but are not limited to, teniposide, etoposide, adriamycin, camptothecin, daunorubicin, dactinomycin, mitoxantrone, amsacrine, epirubicin and idarubicin.

Exemplary taxanes or taxane derivatives include, but are not limited to, paclitaxel and docetaxol.

Exemplary general chemotherapeutic, anti-neoplastic, anti-proliferative agents include, but are not limited to, altretamine (Hexalen); isotretinoin (Accutane; Amnesteem; Claravis; Sotret); tretinoin (Vesanoid); azacitidine (Vidaza); bortezomib (Velcade) asparaginase (Elspar); levamisole (Ergamisol); mitotane (Lysodren); procarbazine (Matulane); pegaspargase (Oncaspar); denileukin diftitox (Ontak); porfimer (Photofrin); aldesleukin (Proleukin); lenalidomide (Revlimid); bexarotene (Targretin); thalidomide (Thalomid); temsirolimus (Torisel); arsenic trioxide (Trisenox); verteporfin (Visudyne); mimosine (Leucenol); (1M tegafur—0.4 M 5-chloro-2,4-dihydroxypyrimidine—1 M potassium oxonate), or lovastatin.

In another aspect, the other therapeutic agent is a chemotherapeutic agent or a cytokine such as G-CSF (granulocyte colony stimulating factor).

In yet another aspect, the other therapeutic agents can be standard chemotherapy combinations such as, but not restricted to, CMF (cyclophosphamide, methotrexate and 5-fluorouracil), CAF (cyclophosphamide, adriamycin and 5-fluorouracil), AC (adriamycin and cyclophosphamide), FEC (5-fluorouracil, epirubicin, and cyclophosphamide), ACT or ATC (adriamycin, cyclophosphamide, and paclitaxel), rituximab, Xeloda (capecitabine), Cisplatin (CDDP), Carboplatin, TS-1 (tegafur, gimestat and otastat potassium at a molar ratio of 1:0.4:1), Camptothecin-11 (CPT-11, Irinotecan or Camptosar™), CHOP (cyclophosphamide, hydroxydaunorubicin, oncovin, and prednisone or prednisolone), R—CHOP (rituximab, cyclophosphamide, hydroxydaunorubicin, oncovin, prednisone or prednisolone), or CMFP (cyclophosphamide, methotrexate, 5-fluorouracil and prednisone).

In another aspect, the other therapeutic agents can be an inhibitor of an enzyme, such as a receptor or non-receptor kinase. Receptor and non-receptor kinases are, for example, tyrosine kinases or serine/threonine kinases. Kinase inhibitors described herein are small molecules, polynucleic acids, polypeptides, or antibodies.

Exemplary kinase inhibitors include, but are not limited to, Bevacizumab (targets VEGF), BIBW 2992 (targets EGFR and Erb2), Cetuximab/Erbitux (targets Erb1), Imatinib/Gleevic (targets Bcr-Abl), Trastuzumab (targets Erb2), Gefitinib/Iressa (targets EGFR), Ranibizumab (targets VEGF), Pegaptanib (targets VEGF), Erlotinib/Tarceva (targets Erb1), Nilotinib (targets Bcr-Abl), Lapatinib (targets Erb1 and Erb2/Her2), GW-572016/lapatinib ditosylate (targets HER2/Erb2), Panitumumab/Vectibix (targets EGFR), Vandetinib (targets RET/VEGFR), E7080 (multiple targets including RET and VEGFR), Herceptin (targets HER2/Erb2), PKI-166 (targets EGFR), Canertinib/CI-1033 (targets EGFR), Sunitinib/SU-11464/Sutent (targets EGFR and FLT3), Matuzumab/Emd7200 (targets EGFR), EKB-569 (targets EGFR), Zd6474 (targets EGFR and VEGFR), PKC-412 (targets VEGR and FLT3), Vatalanib/Ptk787/ZK222584 (targets VEGR), CEP-701 (targets FLT3), SU5614 (targets FLT3), MLN518 (targets FLT3), XL999 (targets FLT3), VX-322 (targets FLT3), Azd0530 (targets SRC), BMS-354825 (targets SRC), SKI-606 (targets SRC), CP-690 (targets JAK), AG-490 (targets JAK), WHI-P154 (targets JAK), WHI-P131 (targets JAK), sorafenib/Nexavar (targets RAF kinase, VEGFR-1, VEGFR-2, VEGFR-3, PDGFR-ß, KIT, FLT-3, and RET), Dasatinib/Sprycel (BCR/ABL and Src), AC-220 (targets Flt3), AC-480 (targets all HER proteins, “panHER”), Motesanib diphosphate (targets VEGF1-3, PDGFR, and c-kit), Denosumab (targets RANKL, inhibits SRC), AMG888 (targets HER3), and AP24534 (multiple targets including Flt3).

Exemplary serine/threonine kinase inhibitors include, but are not limited to, Rapamune (targets mTOR/FRAP1), Deforolimus (targets mTOR), Certican/Everolimus (targets mTOR/FRAP1), AP23573 (targets mTOR/FRAP1), Eril/Fasudil hydrochloride (targets RHO), Flavopiridol (targets CDK), Seliciclib/CYC202/Roscovitrine (targets CDK), SNS-032/BMS-387032 (targets CDK), Ruboxistaurin (targets PKC), Pkc412 (targets PKC), Bryostatin (targets PKC), KAI-9803 (targets PKC), SF1126 (targets P13K), VX-680 (targets Aurora kinase), Azdl 1152 (targets Aurora kinase), Arry-142886/AZD-6244 (targets MAP/MEK), SCIO-469 (targets MAP/MEK), GW681323 (targets MAP/MEK), CC-401 (targets JNK), CEP-1347 (targets JNK), and PD 332991 (targets CDK).

Exemplary tyrosine kinase inhibitors include, but are not limited to, erlotinib (Tarceva); gefitinib (Iressa); imatinib (Gleevec); sorafenib (Nexavar); sunitinib (Sutent); trastuzumab (Herceptin); bevacizumab (Avastin); rituximab (Rituxan); lapatinib (Tykerb); cetuximab (Erbitux); panitumumab (Vectibix); everolimus (Afinitor); alemtuzumab (Campath); gemtuzumab (Mylotarg); temsirolimus (Torisel); pazopanib (Votrient); dasatinib (Sprycel); nilotinib (Tasigna); vatalanib (Ptk787; ZK222584); CEP-701; SU5614; MLN518; XL999; VX-322; Azd0530; BMS-354825; SKI-606 CP-690; AG-490; WHI-P154; WHI-P131; AC-220; or AMG888. More examples of the other therapeutic agents suitable to be used in combination with a compounds of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof are disclosed in co-pending U.S. Application No. 61/992,881 filed May 13, 2014 and International Application No. PCT/US2014/069167 filed Dec. 8, 2014, the contents of each of which are incorporated herein by reference in their entireties.

The present disclosure provides methods for combination therapy in which a composition comprising a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and one or more other therapeutic agents are administered to a subject in need for treatment of a disease or cancer. The combination therapy can also be administered to cancer cells to inhibit proliferation or induce cell death. In one aspect, a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof is administered subsequent to administration of the composition of the present disclosure comprising a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and one or more other therapeutic agents. In one aspect, a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof is administered prior to administration of the composition of the present disclosure comprising a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and one or more other therapeutic agents. In one aspect, a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof is administered subsequent to administration of one or more therapeutic agents, such that the other therapeutic agents are administered either in a single composition or in two or more compositions, e.g. administered simultaneously, sequentially, or in alternation. In one aspect, a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof is administered prior to administration of one or more therapeutic agents, such that the other therapeutic agents are administered either in a single composition or in two or more compositions, e.g. administered simultaneously, sequentially, or in alternation.

In one embodiment, a composition of the present disclosure includes a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and one or more anticancer agents, e.g., CHOP (cyclophosphamide, hydroxydaunorubicin, oncovin, and prednisone or prednisolone) or R—CHOP (rituximab, cyclophosphamide, hydroxydaunorubicin, oncovin, prednisone or prednisolone). In one embodiment, a composition of the present disclosure includes a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and prednisone or prednisolone. Methods of the present disclosure include the combination therapy of administering a compound of Formulae (I)-(VIa) or a pharmaceutically acceptable salt thereof, and anticancer agents, wherein the anticancer agents are CHOP, R—CHOP, prednisone, or prednisolone.

In certain embodiments, “combination therapy” is intended to embrace administration of these therapeutic agents in a sequential manner, wherein each therapeutic agent is administered at a different time, as well as administration of these therapeutic agents, or at least two of the therapeutic agents concurrently, or in a substantially simultaneous manner. Simultaneous administration can be accomplished, for example, by administering to the subject a single capsule having a fixed ratio of each therapeutic agent or in multiple, single capsules for each of the therapeutic agents. Sequential or substantially simultaneous administration of each therapeutic agent can be effected by any appropriate route including, but not limited to, oral routes, intravenous routes, intramuscular routes, and direct absorption through mucous membrane tissues. The therapeutic agents can be administered by the same route or by different routes. For example, a first therapeutic agent of the combination selected may be administered by intravenous injection while the other therapeutic agents of the combination may be administered orally. Alternatively, for example, all therapeutic agents may be administered orally or all therapeutic agents may be administered by intravenous injection. Therapeutic agents may also be administered in alternation.

In certain aspects of the disclosure, the combination therapies featured in the present disclosure can result in a synergistic effect in the treatment of a disease or cancer. A “synergistic effect” is defined as where the efficacy of a combination of therapeutic agents is greater than the sum of the effects of any of the agents given alone. A synergistic effect may also be an effect that cannot be achieved by administration of any of the compounds or other therapeutic agents as single agents. The synergistic effect may include, but is not limited to, an effect of treating cancer by reducing tumor size, inhibiting tumor growth, or increasing survival of the subject. The synergistic effect may also include reducing cancer cell viability, inducing cancer cell death, and inhibiting or delaying cancer cell growth.

In certain aspects of the disclosure “combination therapy” also embraces the administration of the therapeutic agents as described above in further combination with other biologically active ingredients and non-drug therapies (e.g., surgery or radiation treatment). Where the combination therapy further comprises a non-drug treatment, the non-drug treatment may be conducted at any suitable time so long as a beneficial effect from the co-action of the combination of the therapeutic agents and non-drug treatment is achieved. For example, in appropriate cases, the beneficial effect is still achieved when the non-drug treatment is temporally removed from the administration of the therapeutic agents, perhaps by days or even weeks.

In another aspect, a composition of the present disclosure, or a pharmaceutically acceptable salt, solvate, analog or derivative thereof, may be administered in combination with radiation therapy. Radiation therapy can also be administered in combination with a composition of the present disclosure and another chemotherapeutic agent described herein as part of a multiple agent therapy.

Combination therapy can be achieved by administering two or more agents, e.g., a compound of Formulae (I)-(VIa) and one or more other therapeutic agents, each of which is formulated and administered separately, or by administering two or more agents in a single formulation. Other combinations are also encompassed by combination therapy. For example, two agents can be formulated together and administered in conjunction with a separate formulation containing a third agent. While the two or more agents in the combination therapy can be administered simultaneously, they need not be. For example, administration of a first agent (or combination of agents) can precede administration of a second agent (or combination of agents) by minutes, hours, days, or weeks. Thus, the two or more agents can be administered within minutes of each other or within 1, 2, 3, 6, 9, 12, 15, 18, or 24 hours of each other or within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14 days of each other or within 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks of each other. In some cases even longer intervals are possible. While in many cases it is desirable that the two or more agents used in a combination therapy be present in within the patient's body at the same time, this need not be so.

The present disclosure also provides pharmaceutical compositions comprising a compound of Formulae (I)-(VIa) or pharmaceutically acceptable salts thereof, and one or more other therapeutic agents disclosed herein, mixed with pharmaceutically suitable carriers or excipient(s) at doses to treat or prevent a disease or condition as described herein. In one aspect, the present disclosure also provides pharmaceutical compositions comprising any compound of Table I or pharmaceutically acceptable salts thereof, and one or more therapeutic agents, mixed with pharmaceutically suitable carriers or excipient (s) at doses to treat or prevent a disease or condition as described herein. In another aspect, the present disclosure also provides pharmaceutical compositions comprising Compound 44

or pharmaceutically acceptable salts thereof, and one or more therapeutic agents, mixed with pharmaceutically suitable carriers or excipient(s) at doses to treat or prevent a disease or condition as described herein. The pharmaceutical compositions of the present disclosure can also be administered in combination with other therapeutic agents or therapeutic modalities simultaneously, sequentially, or in alternation.

Mixtures of compositions of the present disclosure can also be administered to the patient as a simple mixture or in suitable formulated pharmaceutical compositions. For example, one aspect of the disclosure relates to a pharmaceutical composition comprising a therapeutically effective dose of an EZH2 inhibitor of Formulae (I)-(VIa), or a pharmaceutically acceptable salt, hydrate, enantiomer or stereoisomer thereof; one or more other therapeutic agents, and a pharmaceutically acceptable diluent or carrier.

A “pharmaceutical composition” is a formulation containing the compounds of the present disclosure in a form suitable for administration to a subject. A compound of Formulae (I)-(VIa) and one or more other therapeutic agents described herein each can be formulated individually or in multiple pharmaceutical compositions in any combinations of the active ingredients. Accordingly, one or more administration routes can be properly elected based on the dosage form of each pharmaceutical composition. Alternatively, a compound of Formulae (I)-(VIa) and one or more other therapeutic agents described herein can be formulated as one pharmaceutical composition.

In one embodiment, the pharmaceutical composition is in bulk or in unit dosage form. The unit dosage form is any of a variety of forms, including, for example, a capsule, an IV bag, a tablet, a single pump on an aerosol inhaler or a vial. The quantity of active ingredient (e.g., a formulation of the disclosed compound or salt, hydrate, solvate or isomer thereof) in a unit dose of composition is an effective amount and is varied according to the particular treatment involved. One skilled in the art will appreciate that it is sometimes necessary to make routine variations to the dosage depending on the age and condition of the patient. The dosage will also depend on the route of administration. A variety of routes are contemplated, including oral, pulmonary, rectal, parenteral, transdermal, subcutaneous, intravenous, intramuscular, intraperitoneal, inhalational, buccal, sublingual, intrapleural, intrathecal, intranasal, and the like. Dosage forms for the topical or transdermal administration of a compound of this disclosure include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. In one embodiment, the active compound is mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that are required.

As used herein, the phrase “pharmaceutically acceptable” refers to those compounds, anions, cations, materials, compositions, carriers, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

“Pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic and neither biologically nor otherwise undesirable, and includes excipient that is acceptable for veterinary use as well as human pharmaceutical use. A “pharmaceutically acceptable excipient” as used in the specification and claims includes both one and more than one such excipient.

A pharmaceutical composition of the disclosure is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), and transmucosal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates, and agents for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

A composition of the disclosure can be administered to a subject in many of the well-known methods currently used for chemotherapeutic treatment. For example, for treatment of cancers, a compound of the disclosure may be injected directly into tumors, injected into the blood stream or body cavities or taken orally or applied through the skin with patches. The dose chosen should be sufficient to constitute effective treatment but not so high as to cause unacceptable side effects. The state of the disease condition (e.g., cancer, precancer, and the like) and the health of the patient should preferably be closely monitored during and for a reasonable period after treatment.

The term “therapeutically effective amount”, as used herein, refers to an amount of a pharmaceutical agent to treat, ameliorate, or prevent an identified disease or condition, or to exhibit a detectable therapeutic or inhibitory effect. The effect can be detected by any assay method known in the art. The precise effective amount for a subject will depend upon the subject's body weight, size, and health; the nature and extent of the condition; and the therapeutic or combination of therapeutics selected for administration. Therapeutically effective amounts for a given situation can be determined by routine experimentation that is within the skill and judgment of the clinician. In a preferred aspect, the disease or condition to be treated is cancer. In another aspect, the disease or condition to be treated is a cell proliferative disorder.

In certain embodiments the therapeutically effective amount of each pharmaceutical agent used in combination will be lower when used in combination in comparison to monotherapy with each agent alone. Such lower therapeutically effective amount could afford for lower toxicity of the therapeutic regimen.

For any compound, the therapeutically effective amount can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models, usually rats, mice, rabbits, dogs, or pigs. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. Therapeutic/prophylactic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED₅₀ (the dose therapeutically effective in 50% of the population) and LD₅₀ (the dose lethal to 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD₅₀/ED₅₀. Pharmaceutical compositions that exhibit large therapeutic indices are preferred. The dosage may vary within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.

Dosage and administration are adjusted to provide sufficient levels of the active agent(s) or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation.

The pharmaceutical compositions containing active compounds of the present disclosure may be manufactured in a manner that is generally known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. Pharmaceutical compositions may be formulated in a conventional manner using one or more pharmaceutically acceptable carriers comprising excipients and/or auxiliaries that facilitate processing of the active compounds into preparations that can be used pharmaceutically. Of course, the appropriate formulation is dependent upon the route of administration chosen.

Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile inj ectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringeability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol and sorbitol, and sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an edible pharmaceutically acceptable carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser, which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.

The active compounds can be prepared with pharmaceutically acceptable carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.

It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the disclosure are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved.

In therapeutic applications, the dosages of the EZH2 inhibitor compounds described herein, other therapeutic agents described herein, compositions comprising a compound of Formulae (I)-(VIa) and one or more other therapeutic agents, or the pharmaceutical compositions used in accordance with the disclosure vary depending on the agent, the age, weight, and clinical condition of the recipient patient, and the experience and judgment of the clinician or practitioner administering the therapy, among other factors affecting the selected dosage. Generally, the dose should be sufficient to result in slowing, and preferably regressing, the growth of the tumors and also preferably causing complete regression of the cancer. Dosages can range from about 0.01 mg/kg per day to about 5000 mg/kg per day. In preferred aspects, dosages can range from about 1 mg/kg per day to about 1000 mg/kg per day. In an aspect, the dose will be in the range of about 0.1 mg/day to about 50 g/day; about 0.1 mg/day to about 25 g/day; about 0.1 mg/day to about 10 g/day; about 0.1 mg to about 3 g/day; or about 0.1 mg to about 1 g/day, in single, divided, or continuous doses (which dose may be adjusted for the patient's weight in kg, body surface area in m², and age in years). An effective amount of a pharmaceutical agent is that which provides an objectively identifiable improvement as noted by the clinician or other qualified observer. For example, regression of a tumor in a patient may be measured with reference to the diameter of a tumor. Decrease in the diameter of a tumor indicates regression. Regression is also indicated by failure of tumors to reoccur after treatment has stopped. As used herein, the term “dosage effective manner” refers to amount of an active compound to produce the desired biological effect in a subject or cell.

The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.

The composition of the present disclosure is capable of further forming salts. The composition of the present disclosure is capable of forming more than one salt per molecule, e.g., mono-, di-, tri-. All of these forms are also contemplated within the scope of the claimed disclosure.

As used herein, “pharmaceutically acceptable salts” refer to derivatives of the compounds of the present disclosure wherein the parent compound is modified by making acid or base salts thereof. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines, alkali or organic salts of acidic residues such as carboxylic acids, and the like. The pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. For example, such conventional non-toxic salts include, but are not limited to, those derived from inorganic and organic acids selected from 2-acetoxybenzoic, 2-hydroxyethane sulfonic, acetic, ascorbic, benzene sulfonic, benzoic, bicarbonic, carbonic, citric, edetic, ethane disulfonic, 1,2-ethane sulfonic, fumaric, glucoheptonic, gluconic, glutamic, glycolic, glycollyarsanilic, hexylresorcinic, hydrabamic, hydrobromic, hydrochloric, hydroiodic, hydroxymaleic, hydroxynaphthoic, isethionic, lactic, lactobionic, lauryl sulfonic, maleic, malic, mandelic, methane sulfonic, napsylic, nitric, oxalic, pamoic, pantothenic, phenylacetic, phosphoric, polygalacturonic, propionic, salicyclic, stearic, subacetic, succinic, sulfamic, sulfanilic, sulfuric, tannic, tartaric, toluene sulfonic, and the commonly occurring amine acids, e.g., glycine, alanine, phenylalanine, arginine, etc.

Other examples of pharmaceutically acceptable salts include hexanoic acid, cyclopentane propionic acid, pyruvic acid, malonic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, 4-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, 4-toluenesulfonic acid, camphorsulfonic acid, 4-methylbicyclo-[2.2.2]-oct-2-ene-1-carboxylic acid, 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, muconic acid, and the like. The present disclosure also encompasses salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base such as ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.

It should be understood that all references to pharmaceutically acceptable salts include solvent addition forms (solvates), of the same salt.

The composition of the present disclosure may also be prepared as esters, for example, pharmaceutically acceptable esters. For example, a carboxylic acid function group in a compound can be converted to its corresponding ester, e.g., a methyl, ethyl or other ester. Also, an alcohol group in a compound can be converted to its corresponding ester, e.g., acetate, propionate or other ester.

The composition, or pharmaceutically acceptable salts or solvatesthereof, are administered orally, nasally, transdermally, pulmonary, inhalationally, buccally, sublingually, intraperintoneally, subcutaneously, intramuscularly, intravenously, rectally, intrapleurally, intrathecally and parenterally. In one embodiment, the compound is administered orally. One skilled in the art will recognize the advantages of certain routes of administration.

The dosage regimen utilizing the compounds is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal and hepatic function of the patient; and the particular compound or salt thereof employed. An ordinarily skilled physician or veterinarian can readily determine and prescribe the effective amount of the drug required to prevent, counter, or arrest the progress of the condition.

Techniques for formulation and administration of the disclosed compounds of the disclosure can be found in Remington: the Science and Practice of Pharmacy, 19^(th) edition, Mack Publishing Co., Easton, Pa. (1995). In an embodiment, the compounds described herein, and the pharmaceutically acceptable salts thereof, are used in pharmaceutical preparations in combination with a pharmaceutically acceptable carrier or diluent. Suitable pharmaceutically acceptable carriers include inert solid fillers or diluents and sterile aqueous or organic solutions. The compounds will be present in such pharmaceutical compositions in amounts sufficient to provide the desired dosage amount in the range described herein.

All percentages and ratios used herein, unless otherwise indicated, are by weight. Other features and advantages of the present invention are apparent from the different examples. The provided examples illustrate different components and methodology useful in practicing the present invention. The examples do not limit the claimed invention. Based on the present disclosure the skilled artisan can identify and employ other components and methodology useful for practicing the present invention.

The present disclosure provides compositions and methods for treating conditions and diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, wherein said methylation status is mediated at least in part by the activity of EZH2. Modulation of the methylation status of histones can in turn influence the level of expression of target genes activated by methylation, and/or target genes suppressed by methylation. The method includes administering to a subject in need of such treatment, a therapeutically effective amount of a composition of the present disclosure or a pharmaceutically acceptable salt or solvate thereof, to a subject in need of such treatment.

Based at least on the fact that abnormal histone methylation has been found to be associated with certain cancers and precancerous conditions, a method for treating cancer or a precancerous condition with a mutant EZH2 in a subject comprises administering to the subject in need thereof a therapeutically effective amount of a compound that inhibits methylation. In one embodiment a method for treating cancer or a precancerous condition in a subject comprises administering to the subject in need thereof a therapeutically effective amount of a compound that inhibits conversion of unmethylated H3-K27 to monomethylated H3-K27 (H3-K27me1). In one embodiment a method for treating cancer or a precancerous condition in a subject comprises administering to the subject in need thereof a therapeutically effective amount of a compound that inhibits conversion of monomethylated H3-K27 (H3-K27me1) to dimethylated H3-K27 (H3-K27me2). In one embodiment a method for treating cancer or a precancerous condition in a subject comprises administering to the subject in need thereof a therapeutically effective amount of a compound that inhibits conversion of H3-K27me2 to trimethylated H3-K27 (H3-K27me3). In one embodiment a method for treating cancer or a precancerous condition in a subject comprises administering to the subject in need thereof a therapeutically effective amount of a compound that inhibits both conversion of H3-K27me1 to H3-K27me2 and conversion of H3-K27me2 to H3-K27me3. It is important to note that disease-specific increase in methylation can occur at chromatin in key genomic loci in the absence of a global increase in cellular levels of histone or protein methylation. For example, it is possible for aberrant hypermethylation at key disease-relevant genes to occur against a backdrop of global histone or protein hypomethylation.

Modulators of methylation can be used for modulating cell proliferation, generally. For example, in some cases excessive proliferation may be reduced with agents that decrease methylation, whereas insufficient proliferation may be stimulated with agents that increase methylation. Accordingly, diseases that may be treated include hyperproliferative diseases, such as benign cell growth and malignant cell growth (cancer).

The disorder in which EZH2-mediated protein methylation plays a part can be cancer, a cell proliferative disorder, or a precancerous condition. The present disclosure further provides the use of a composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, to a subject in need of such treatment, for the preparation of a medicament useful for the treatment of cancer. Exemplary cancers that may be treated include lymphomas, including non-Hodgkin lymphoma, follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL); melanoma; and leukemia, including CML. Exemplary precancerous condition includes myelodisplastic syndrome (MDS; formerly known as preleukemia).

In general, compounds that are methylation modulators can be used for modulating cell proliferation, generally. For example, in some cases excessive proliferation may be reduced with agents that decrease methylation, whereas insufficient proliferation may be stimulated with agents that increase methylation. Accordingly, diseases that may be treated by the compounds of the disclosure include hyperproliferative diseases, such as benign cell growth and malignant cell growth.

As used herein, a “subject in need thereof” is a subject having a disorder in which EZH2-mediated protein methylation plays a part, or a subject having an increased risk of developing such disorder relative to the population at large. A subject in need thereof can have a precancerous condition. Preferably, a subject in need thereof has cancer. A “subject” includes a mammal. The mammal can be e.g., any mammal, e.g., a human, primate, bird, mouse, rat, fowl, dog, cat, cow, horse, goat, camel, sheep or a pig. Preferably, the mammal is a human.

The subject of the present disclosure includes any human subject who has been diagnosed with, has symptoms of, or is at risk of developing a cancer or a precancerous condition. The subject of the present disclosure includes any human subject expressing a mutant EZH2. For example, a mutant EZH2 comprises one or more mutations, wherein the mutation is a substitution, a point mutation, a nonsense mutation, a missense mutation, a deletion, or an insertion or any other EZH2 mutation described herein.

A subject in need thereof may have refractory or resistant cancer. “Refractory or resistant cancer” means cancer that does not respond to treatment. The cancer may be resistant at the beginning of treatment or it may become resistant during treatment. In some embodiments, the subject in need thereof has cancer recurrence following remission on most recent therapy. In some embodiments, the subject in need thereof received and failed all known effective therapies for cancer treatment. In some embodiments, the subject in need thereof received at least one prior therapy. In certain embodiments the prior therapy is monotherapy. In certain embodiments the prior therapy is combination therapy.

In some embodiments, a subject in need thereof may have a secondary cancer as a result of a previous therapy. “Secondary cancer” means cancer that arises due to or as a result from previous carcinogenic therapies, such as chemotherapy.

The subject may also exhibit resistance to EZH2 histone methyltransferase inhibitors or any other therapeutic agent.

The disclosure also features a method of selecting a combination therapy for a subject having cancer. The method includes the steps of: detecting one or more EZH2 mutations described herein in a sample from the subject; and selecting, based on the presence of the one or more EZH2 mutations, a combination therapy for treating cancer. In one embodiment, the therapy includes administering to the subject a composition of the disclosure. In one embodiment, the method further includes administrating to the subject a therapeutically effective amount of a composition of the disclosure. An EZH2 mutation can be detected using any suitable method known in the art. More methods are described in U.S. patent publication US 20130040906, which is incorporated herein by reference in their entireties.

The methods and uses described herein may include steps of detecting one or more EZH2 mutations described herein in a sample from a subject in need thereof prior to and/or after the administration of a composition of the disclosure (e.g., a composition comprising a compound of Formulae (I)-(VIa) or pharmaceutically acceptable salts thereof, and one or more therapeutic agents) to the subject. The presence of the one or more EZH2 mutations described herein in the tested sample indicates the subject is responsive to the combination therapy of the disclosure.

The present disclosure provides personalized medicine, treatment and/or cancer management for a subject by genetic screening of one or more EZH2 mutations described herein in the subject. For example, the present disclosure provides methods for treating or alleviating a symptom of cancer or a precancerous condition in a subject in need thereof by determining responsiveness of the subject to a combination therapy and when the subject is responsive to the combination therapy, administering to the subject a composition of the disclosure. The responsiveness is determined by obtaining a sample from the subject and detecting one or more EZH2 mutations described herein, and the presence of such one or more EZH2 mutations described herein indicates that the subject is responsive to the composition of the disclosure. Once the responsiveness of a subject is determined, a therapeutically effective amount of a composition, for example, a composition comprising a compound of Formulae (I)-(VIa) or pharmaceutically acceptable salts thereof, and one or more therapeutic agents, can be administered. The therapeutically effective amount of a composition can be determined by one of ordinary skill in the art.

As used herein, the term “responsiveness” is interchangeable with terms “responsive”, “sensitive”, and “sensitivity”, and it is meant that a subject is showing therapeutic responses when administered a composition of the disclosure, e.g., tumor cells or tumor tissues of the subject undergo apoptosis and/or necrosis, and/or display reduced growing, dividing, or proliferation. This term is also meant that a subject will or has a higher probability, relative to the population at large, of showing therapeutic responses when administered a composition of the disclosure, e.g., tumor cells or tumor tissues of the subject undergo apoptosis and/or necrosis, and/or display reduced growing, dividing, or proliferation.

By “sample” it means any biological sample derived from the subject, includes but is not limited to, cells, tissues samples, body fluids (including, but not limited to, mucus, blood, plasma, serum, urine, saliva, and semen), tumor cells, and tumor tissues. Preferably, the sample is selected from bone marrow, peripheral blood cells, blood, plasma and serum. Samples can be provided by the subject under treatment or testing. Alternatively samples can be obtained by the physician according to routine practice in the art.

As used herein, the term “cell proliferative disorder” refers to conditions in which unregulated or abnormal growth, or both, of cells can lead to the development of an unwanted condition or disease, which may or may not be cancerous. Exemplary cell proliferative disorders of the disclosure encompass a variety of conditions wherein cell division is deregulated. Exemplary cell proliferative disorder include, but are not limited to, neoplasms, benign tumors, malignant tumors, pre-cancerous conditions, in situ tumors, encapsulated tumors, metastatic tumors, liquid tumors, solid tumors, immunological tumors, hematological tumors, cancers, carcinomas, leukemias, lymphomas, sarcomas, and rapidly dividing cells. The term “rapidly dividing cell” as used herein is defined as any cell that divides at a rate that exceeds or is greater than what is expected or observed among neighboring or juxtaposed cells within the same tissue. A cell proliferative disorder includes a precancer or a precancerous condition. A cell proliferative disorder includes cancer. Preferably, the methods provided herein are used to treat or alleviate a symptom of cancer. The term “cancer” includes solid tumors, as well as, hematologic tumors and/or malignancies. A “precancer cell” or “precancerous cell” is a cell manifesting a cell proliferative disorder that is a precancer or a precancerous condition. A “cancer cell” or “cancerous cell” is a cell manifesting a cell proliferative disorder that is a cancer. Any reproducible means of measurement may be used to identify cancer cells or precancerous cells. Cancer cells or precancerous cells can be identified by histological typing or grading of a tissue sample (e.g., a biopsy sample). Cancer cells or precancerous cells can be identified through the use of appropriate molecular markers.

Exemplary non-cancerous conditions or disorders include, but are not limited to, rheumatoid arthritis; inflammation; autoimmune disease; lymphoproliferative conditions; acromegaly; rheumatoid spondylitis; osteoarthritis; gout, other arthritic conditions; sepsis; septic shock; endotoxic shock; gram-negative sepsis; toxic shock syndrome; asthma; adult respiratory distress syndrome; chronic obstructive pulmonary disease; chronic pulmonary inflammation; inflammatory bowel disease; Crohn's disease; psoriasis; eczema; ulcerative colitis; pancreatic fibrosis; hepatic fibrosis; acute and chronic renal disease; irritable bowel syndrome; pyresis; restenosis; cerebral malaria; stroke and ischemic injury; neural trauma; Alzheimer's disease; Huntington's disease; Parkinson's disease; acute and chronic pain; allergic rhinitis; allergic conjunctivitis; chronic heart failure; acute coronary syndrome; cachexia; malaria; leprosy; leishmaniasis; Lyme disease; Reiter's syndrome; acute synovitis; muscle degeneration, bursitis; tendonitis; tenosynovitis; herniated, ruptures, or prolapsed intervertebral disk syndrome; osteopetrosis; thrombosis; restenosis; silicosis; pulmonary sarcosis; bone resorption diseases, such as osteoporosis; graft-versus-host reaction; Multiple Sclerosis; lupus; fibromyalgia; AIDS and other viral diseases such as Herpes Zoster, Herpes Simplex I or II, influenza virus and cytomegalovirus; and diabetes mellitus.

Exemplary cancers include, but are not limited to, adrenocortical carcinoma, AIDS-related cancers, AIDS-related lymphoma, anal cancer, anorectal cancer, cancer of the anal canal, appendix cancer, childhood cerebellar astrocytoma, childhood cerebral astrocytoma, basal cell carcinoma, skin cancer (non-melanoma), biliary cancer, extrahepatic bile duct cancer, intrahepatic bile duct cancer, bladder cancer, urinary bladder cancer, bone and joint cancer, osteosarcoma and malignant fibrous histiocytoma, brain cancer, brain tumor, brain stem glioma, cerebellar astrocytoma, cerebral astrocytoma/malignant glioma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumors, visual pathway and hypothalamic glioma, breast cancer, bronchial adenomas/carcinoids, carcinoid tumor, gastrointestinal, nervous system cancer, nervous system lymphoma, central nervous system cancer, central nervous system lymphoma, cervical cancer, childhood cancers, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloproliferative disorders, colon cancer, colorectal cancer, cutaneous T-cell lymphoma, lymphoid neoplasm, mycosis fungoides, Seziary Syndrome, endometrial cancer, esophageal cancer, extracranial germ cell tumor, extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer, intraocular melanoma, retinoblastoma, gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor (GIST), germ cell tumor, ovarian germ cell tumor, gestational trophoblastic tumor glioma, head and neck cancer, hepatocellular (liver) cancer, Hodgkin lymphoma, hypopharyngeal cancer, intraocular melanoma, ocular cancer, islet cell tumors (endocrine pancreas), Kaposi Sarcoma, kidney cancer, renal cancer, kidney cancer, laryngeal cancer, acute lymphoblastic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, hairy cell leukemia, lip and oral cavity cancer, liver cancer, lung cancer, non-small cell lung cancer, small cell lung cancer, AIDS-related lymphoma, non-Hodgkin lymphoma, primary central nervous system lymphoma, Waldenstram macroglobulinemia, medulloblastoma, melanoma, intraocular (eye) melanoma, merkel cell carcinoma, mesothelioma malignant, mesothelioma, metastatic squamous neck cancer, mouth cancer, cancer of the tongue, multiple endocrine neoplasia syndrome, mycosis fungoides, myelodysplastic syndromes, myelodysplastic/myeloproliferative diseases, chronic myelogenous leukemia, acute myeloid leukemia, multiple myeloma, chronic myeloproliferative disorders, nasopharyngeal cancer, neuroblastoma, oral cancer, oral cavity cancer, oropharyngeal cancer, ovarian cancer, ovarian epithelial cancer, ovarian low malignant potential tumor, pancreatic cancer, islet cell pancreatic cancer, paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pineoblastoma and supratentorial primitive neuroectodermal tumors, pituitary tumor, plasma cell neoplasm/multiple myeloma, pleuropulmonary blastoma, prostate cancer, rectal cancer, renal pelvis and ureter, transitional cell cancer, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, ewing family of sarcoma tumors, Kaposi Sarcoma, soft tissue sarcoma, uterine cancer, uterine sarcoma, skin cancer (non-melanoma), skin cancer (melanoma), merkel cell skin carcinoma, small intestine cancer, soft tissue sarcoma, squamous cell carcinoma, stomach (gastric) cancer, supratentorial primitive neuroectodermal tumors, testicular cancer, throat cancer, thymoma, thymoma and thymic carcinoma, thyroid cancer, transitional cell cancer of the renal pelvis and ureter and other urinary organs, gestational trophoblastic tumor, urethral cancer, endometrial uterine cancer, uterine sarcoma, uterine corpus cancer, vaginal cancer, vulvar cancer, and Wilm's Tumor.

A “cell proliferative disorder of the hematologic system” is a cell proliferative disorder involving cells of the hematologic system. A cell proliferative disorder of the hematologic system can include lymphoma, leukemia, myeloid neoplasms, mast cell neoplasms, myelodysplasia, benign monoclonal gammopathy, lymphomatoid granulomatosis, lymphomatoid papulosis, polycythemia vera, chronic myelocytic leukemia, agnogenic myeloid metaplasia, and essential thrombocythemia. A cell proliferative disorder of the hematologic system can include hyperplasia, dysplasia, and metaplasia of cells of the hematologic system. Preferably, compositions of the present disclosure may be used to treat a cancer selected from the group consisting of a hematologic cancer of the present disclosure or a hematologic cell proliferative disorder of the present disclosure. A hematologic cancer of the present disclosure can include multiple myeloma, lymphoma (including Hodgkin's lymphoma, non-Hodgkin's lymphoma, childhood lymphomas, and lymphomas of lymphocytic and cutaneous origin), leukemia (including childhood leukemia, hairy-cell leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, chronic lymphocytic leukemia, chronic myelocytic leukemia, chronic myelogenous leukemia, and mast cell leukemia), myeloid neoplasms and mast cell neoplasms.

A “cell proliferative disorder of the lung” is a cell proliferative disorder involving cells of the lung. Cell proliferative disorders of the lung can include all forms of cell proliferative disorders affecting lung cells. Cell proliferative disorders of the lung can include lung cancer, a precancer or precancerous condition of the lung, benign growths or lesions of the lung, and malignant growths or lesions of the lung, and metastatic lesions in tissue and organs in the body other than the lung. Preferably, compositions of the present disclosure may be used to treat lung cancer or cell proliferative disorders of the lung. Lung cancer can include all forms of cancer of the lung. Lung cancer can include malignant lung neoplasms, carcinoma in situ, typical carcinoid tumors, and atypical carcinoid tumors. Lung cancer can include small cell lung cancer (“SCLC”), non-small cell lung cancer (“NSCLC”), squamous cell carcinoma, adenocarcinoma, small cell carcinoma, large cell carcinoma, adenosquamous cell carcinoma, and mesothelioma. Lung cancer can include “scar carcinoma,” bronchioalveolar carcinoma, giant cell carcinoma, spindle cell carcinoma, and large cell neuroendocrine carcinoma. Lung cancer can include lung neoplasms having histologic and ultrastructural heterogeneity (e.g., mixed cell types).

Cell proliferative disorders of the lung can include all forms of cell proliferative disorders affecting lung cells. Cell proliferative disorders of the lung can include lung cancer, precancerous conditions of the lung. Cell proliferative disorders of the lung can include hyperplasia, metaplasia, and dysplasia of the lung. Cell proliferative disorders of the lung can include asbestos-induced hyperplasia, squamous metaplasia, and benign reactive mesothelial metaplasia. Cell proliferative disorders of the lung can include replacement of columnar epithelium with stratified squamous epithelium, and mucosal dysplasia. Individuals exposed to inhaled injurious environmental agents such as cigarette smoke and asbestos may be at increased risk for developing cell proliferative disorders of the lung. Prior lung diseases that may predispose individuals to development of cell proliferative disorders of the lung can include chronic interstitial lung disease, necrotizing pulmonary disease, scleroderma, rheumatoid disease, sarcoidosis, interstitial pneumonitis, tuberculosis, repeated pneumonias, idiopathic pulmonary fibrosis, granulomata, asbestosis, fibrosing alveolitis, and Hodgkin's disease.

A “cell proliferative disorder of the colon” is a cell proliferative disorder involving cells of the colon. Preferably, the cell proliferative disorder of the colon is colon cancer. Preferably, compositions of the present disclosure may be used to treat colon cancer or cell proliferative disorders of the colon. Colon cancer can include all forms of cancer of the colon. Colon cancer can include sporadic and hereditary colon cancers. Colon cancer can include malignant colon neoplasms, carcinoma in situ, typical carcinoid tumors, and atypical carcinoid tumors. Colon cancer can include adenocarcinoma, squamous cell carcinoma, and adenosquamous cell carcinoma. Colon cancer can be associated with a hereditary syndrome selected from the group consisting of hereditary nonpolyposis colorectal cancer, familial adenomatous polyposis, Gardner's syndrome, Peutz-Jeghers syndrome, Turcot's syndrome and juvenile polyposis. Colon cancer can be caused by a hereditary syndrome selected from the group consisting of hereditary nonpolyposis colorectal cancer, familial adenomatous polyposis, Gardner's syndrome, Peutz-Jeghers syndrome, Turcot's syndrome and juvenile polyposis.

Cell proliferative disorders of the colon can include all forms of cell proliferative disorders affecting colon cells. Cell proliferative disorders of the colon can include colon cancer, precancerous conditions of the colon, adenomatous polyps of the colon and metachronous lesions of the colon. A cell proliferative disorder of the colon can include adenoma. Cell proliferative disorders of the colon can be characterized by hyperplasia, metaplasia, and dysplasia of the colon. Prior colon diseases that may predispose individuals to development of cell proliferative disorders of the colon can include prior colon cancer. Current disease that may predispose individuals to development of cell proliferative disorders of the colon can include Crohn's disease and ulcerative colitis. A cell proliferative disorder of the colon can be associated with a mutation in a gene selected from the group consisting of p53, ras, FAP and DCC. An individual can have an elevated risk of developing a cell proliferative disorder of the colon due to the presence of a mutation in a gene selected from the group consisting of p53, ras, FAP and DCC.

A “cell proliferative disorder of the pancreas” is a cell proliferative disorder involving cells of the pancreas. Cell proliferative disorders of the pancreas can include all forms of cell proliferative disorders affecting pancreatic cells. Cell proliferative disorders of the pancreas can include pancreas cancer, a precancer or precancerous condition of the pancreas, hyperplasia of the pancreas, and dysaplasia of the pancreas, benign growths or lesions of the pancreas, and malignant growths or lesions of the pancreas, and metastatic lesions in tissue and organs in the body other than the pancreas. Pancreatic cancer includes all forms of cancer of the pancreas. Pancreatic cancer can include ductal adenocarcinoma, adenosquamous carcinoma, pleomorphic giant cell carcinoma, mucinous adenocarcinoma, osteoclast-like giant cell carcinoma, mucinous cystadenocarcinoma, acinar carcinoma, unclassified large cell carcinoma, small cell carcinoma, pancreatoblastoma, papillary neoplasm, mucinous cystadenoma, papillary cystic neoplasm, and serous cystadenoma. Pancreatic cancer can also include pancreatic neoplasms having histologic and ultrastructural heterogeneity (e.g., mixed cell types).

A “cell proliferative disorder of the prostate” is a cell proliferative disorder involving cells of the prostate. Cell proliferative disorders of the prostate can include all forms of cell proliferative disorders affecting prostate cells. Cell proliferative disorders of the prostate can include prostate cancer, a precancer or precancerous condition of the prostate, benign growths or lesions of the prostate, and malignant growths or lesions of the prostate, and metastatic lesions in tissue and organs in the body other than the prostate. Cell proliferative disorders of the prostate can include hyperplasia, metaplasia, and dysplasia of the prostate.

A “cell proliferative disorder of the skin” is a cell proliferative disorder involving cells of the skin. Cell proliferative disorders of the skin can include all forms of cell proliferative disorders affecting skin cells. Cell proliferative disorders of the skin can include a precancer or precancerous condition of the skin, benign growths or lesions of the skin, melanoma, malignant melanoma and other malignant growths or lesions of the skin, and metastatic lesions in tissue and organs in the body other than the skin. Cell proliferative disorders of the skin can include hyperplasia, metaplasia, and dysplasia of the skin.

A “cell proliferative disorder of the ovary” is a cell proliferative disorder involving cells of the ovary. Cell proliferative disorders of the ovary can include all forms of cell proliferative disorders affecting cells of the ovary. Cell proliferative disorders of the ovary can include a precancer or precancerous condition of the ovary, benign growths or lesions of the ovary, ovarian cancer, malignant growths or lesions of the ovary, and metastatic lesions in tissue and organs in the body other than the ovary. Cell proliferative disorders of the skin can include hyperplasia, metaplasia, and dysplasia of cells of the ovary.

A “cell proliferative disorder of the breast” is a cell proliferative disorder involving cells of the breast. Cell proliferative disorders of the breast can include all forms of cell proliferative disorders affecting breast cells. Cell proliferative disorders of the breast can include breast cancer, a precancer or precancerous condition of the breast, benign growths or lesions of the breast, and malignant growths or lesions of the breast, and metastatic lesions in tissue and organs in the body other than the breast. Cell proliferative disorders of the breast can include hyperplasia, metaplasia, and dysplasia of the breast.

A cell proliferative disorder of the breast can be a precancerous condition of the breast. Compositions of the present disclosure may be used to treat a precancerous condition of the breast. A precancerous condition of the breast can include atypical hyperplasia of the breast, ductal carcinoma in situ (DCIS), intraductal carcinoma, lobular carcinoma in situ (LCIS), lobular neoplasia, and stage 0 or grade 0 growth or lesion of the breast (e.g., stage 0 or grade 0 breast cancer, or carcinoma in situ). A precancerous condition of the breast can be staged according to the TNM classification scheme as accepted by the American Joint Committee on Cancer (AJCC), where the primary tumor (T) has been assigned a stage of T0 or Tis; and where the regional lymph nodes (N) have been assigned a stage of NO; and where distant metastasis (M) has been assigned a stage of M0.

The cell proliferative disorder of the breast can be breast cancer. Preferably, compositions of the present disclosure may be used to treat breast cancer. Breast cancer includes all forms of cancer of the breast. Breast cancer can include primary epithelial breast cancers. Breast cancer can include cancers in which the breast is involved by other tumors such as lymphoma, sarcoma or melanoma. Breast cancer can include carcinoma of the breast, ductal carcinoma of the breast, lobular carcinoma of the breast, undifferentiated carcinoma of the breast, cystosarcoma phyllodes of the breast, angiosarcoma of the breast, and primary lymphoma of the breast. Breast cancer can include Stage I, II, IIIA, IIIB, IIIC and IV breast cancer. Ductal carcinoma of the breast can include invasive carcinoma, invasive carcinoma in situ with predominant intraductal component, inflammatory breast cancer, and a ductal carcinoma of the breast with a histologic type selected from the group consisting of comedo, mucinous (colloid), medullary, medullary with lymphocytic infiltrate, papillary, scirrhous, and tubular. Lobular carcinoma of the breast can include invasive lobular carcinoma with predominant in situ component, invasive lobular carcinoma, and infiltrating lobular carcinoma. Breast cancer can include Paget's disease, Paget's disease with intraductal carcinoma, and Paget's disease with invasive ductal carcinoma. Breast cancer can include breast neoplasms having histologic and ultrastructural heterogeneity (e.g., mixed cell types).

Preferably, compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, may be used to treat breast cancer. A breast cancer that is to be treated can include familial breast cancer. A breast cancer that is to be treated can include sporadic breast cancer. A breast cancer that is to be treated can arise in a male subject. A breast cancer that is to be treated can arise in a female subject. A breast cancer that is to be treated can arise in a premenopausal female subject or a postmenopausal female subject. A breast cancer that is to be treated can arise in a subject equal to or older than 30 years old, or a subject younger than 30 years old. A breast cancer that is to be treated has arisen in a subject equal to or older than 50 years old, or a subject younger than 50 years old. A breast cancer that is to be treated can arise in a subject equal to or older than 70 years old, or a subject younger than 70 years old.

A breast cancer that is to be treated can be typed to identify a familial or spontaneous mutation in BRCA1, BRCA2, or p53. A breast cancer that is to be treated can be typed as having a HER2/neu gene amplification, as overexpressing HER2/neu, or as having a low, intermediate or high level of HER2/neu expression. A breast cancer that is to be treated can be typed for a marker selected from the group consisting of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor-2, Ki-67, CA15-3, CA 27-29, and c-Met. A breast cancer that is to be treated can be typed as ER-unknown, ER-rich or ER-poor. A breast cancer that is to be treated can be typed as ER-negative or ER-positive. ER-typing of a breast cancer may be performed by any reproducible means. ER-typing of a breast cancer may be performed as set forth in Onkologie 27: 175-179 (2004). A breast cancer that is to be treated can be typed as PR-unknown, PR-rich, or PR-poor. A breast cancer that is to be treated can be typed as PR-negative or PR-positive. A breast cancer that is to be treated can be typed as receptor positive or receptor negative. A breast cancer that is to be treated can be typed as being associated with elevated blood levels of CA 15-3, or CA 27-29, or both.

A breast cancer that is to be treated can include a localized tumor of the breast. A breast cancer that is to be treated can include a tumor of the breast that is associated with a negative sentinel lymph node (SLN) biopsy. A breast cancer that is to be treated can include a tumor of the breast that is associated with a positive sentinel lymph node (SLN) biopsy. A breast cancer that is to be treated can include a tumor of the breast that is associated with one or more positive axillary lymph nodes, where the axillary lymph nodes have been staged by any applicable method. A breast cancer that is to be treated can include a tumor of the breast that has been typed as having nodal negative status (e.g., node-negative) or nodal positive status (e.g., node-positive). A breast cancer that is to be treated can include a tumor of the breast that has metastasized to other locations in the body. A breast cancer that is to be treated can be classified as having metastasized to a location selected from the group consisting of bone, lung, liver, or brain. A breast cancer that is to be treated can be classified according to a characteristic selected from the group consisting of metastatic, localized, regional, local-regional, locally advanced, distant, multicentric, bilateral, ipsilateral, contralateral, newly diagnosed, recurrent, and inoperable.

A compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, may be used to treat or prevent a cell proliferative disorder of the breast, or to treat or prevent breast cancer, in a subject having an increased risk of developing breast cancer relative to the population at large. A subject with an increased risk of developing breast cancer relative to the population at large is a female subject with a family history or personal history of breast cancer. A subject with an increased risk of developing breast cancer relative to the population at large is a female subject having a germ-line or spontaneous mutation in BRCA1 or BRCA2, or both. A subject with an increased risk of developing breast cancer relative to the population at large is a female subject with a family history of breast cancer and a germ-line or spontaneous mutation in BRCA1 or BRCA2, or both. A subject with an increased risk of developing breast cancer relative to the population at large is a female who is greater than 30 years old, greater than 40 years old, greater than 50 years old, greater than 60 years old, greater than 70 years old, greater than 80 years old, or greater than 90 years old. A subject with an increased risk of developing breast cancer relative to the population at large is a subject with atypical hyperplasia of the breast, ductal carcinoma in situ (DCIS), intraductal carcinoma, lobular carcinoma in situ (LCIS), lobular neoplasia, or a stage 0 growth or lesion of the breast (e.g., stage 0 or grade 0 breast cancer, or carcinoma in situ).

A breast cancer that is to be treated can be histologically graded according to the Scarff-Bloom-Richardson system, wherein a breast tumor has been assigned a mitosis count score of 1, 2, or 3; a nuclear pleiomorphism score of 1, 2, or 3; a tubule formation score of 1, 2, or 3; and a total Scarff-Bloom-Richardson score of between 3 and 9. A breast cancer that is to be treated can be assigned a tumor grade according to the International Consensus Panel on the Treatment of Breast Cancer selected from the group consisting of grade 1, grade 1-2, grade 2, grade 2-3, or grade 3.

A cancer that is to be treated can be staged according to the American Joint Committee on Cancer (AJCC) TNM classification system, where the tumor (T) has been assigned a stage of TX, T1, T1mic, T1a, T1b, T1c, T2, T3, T4, T4a, T4b, T4c, or T4d; and where the regional lymph nodes (N) have been assigned a stage of NX, N0, N1, N2, N2a, N2b, N3, N3a, N3b, or N3c; and where distant metastasis (M) can be assigned a stage of MX, M0, or M1. A cancer that is to be treated can be staged according to an American Joint Committee on Cancer (AJCC) classification as Stage I, Stage IIA, Stage IIB, Stage IIIA, Stage IIIB, Stage IIIC, or Stage IV. A cancer that is to be treated can be assigned a grade according to an AJCC classification as Grade GX (e.g., grade cannot be assessed), Grade 1, Grade 2, Grade 3 or Grade 4. A cancer that is to be treated can be staged according to an AJCC pathologic classification (pN) of pNX, pN0, PN0 (I−), PN0 (I+), PN0 (mol−), PN0 (mol+), PN1, PN1(mi), PN1a, PN1b, PN1c, pN2, pN2a, pN2b, pN3, pN3a, pN3b, or pN3c.

A cancer that is to be treated can include a tumor that has been determined to be less than or equal to about 2 centimeters in diameter. A cancer that is to be treated can include a tumor that has been determined to be from about 2 to about 5 centimeters in diameter. A cancer that is to be treated can include a tumor that has been determined to be greater than or equal to about 3 centimeters in diameter. A cancer that is to be treated can include a tumor that has been determined to be greater than 5 centimeters in diameter. A cancer that is to be treated can be classified by microscopic appearance as well differentiated, moderately differentiated, poorly differentiated, or undifferentiated. A cancer that is to be treated can be classified by microscopic appearance with respect to mitosis count (e.g., amount of cell division) or nuclear pleiomorphism (e.g., change in cells). A cancer that is to be treated can be classified by microscopic appearance as being associated with areas of necrosis (e.g., areas of dying or degenerating cells). A cancer that is to be treated can be classified as having an abnormal karyotype, having an abnormal number of chromosomes, or having one or more chromosomes that are abnormal in appearance. A cancer that is to be treated can be classified as being aneuploid, triploid, tetraploid, or as having an altered ploidy. A cancer that is to be treated can be classified as having a chromosomal translocation, or a deletion or duplication of an entire chromosome, or a region of deletion, duplication or amplification of a portion of a chromosome.

A cancer that is to be treated can be evaluated by DNA cytometry, flow cytometry, or image cytometry. A cancer that is to be treated can be typed as having 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of cells in the synthesis stage of cell division (e.g., in S phase of cell division). A cancer that is to be treated can be typed as having a low S-phase fraction or a high S-phase fraction.

As used herein, a “normal cell” is a cell that cannot be classified as part of a “cell proliferative disorder”. A normal cell lacks unregulated or abnormal growth, or both, that can lead to the development of an unwanted condition or disease. Preferably, a normal cell possesses normally functioning cell cycle checkpoint control mechanisms.

As used herein, “contacting a cell” refers to a condition in which a compound or other composition of matter is in direct contact with a cell, or is close enough to induce a desired biological effect in a cell.

As used herein, “candidate compound” refers to a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, that has been or will be tested in one or more in vitro or in vivo biological assays, in order to determine if that compound is likely to elicit a desired biological or medical response in a cell, tissue, system, animal or human that is being sought by a researcher or clinician. A candidate compound is a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof. The biological or medical response can be the treatment of cancer. The biological or medical response can be treatment or prevention of a cell proliferative disorder. In vitro or in vivo biological assays can include, but are not limited to, enzymatic activity assays, electrophoretic mobility shift assays, reporter gene assays, in vitro cell viability assays, and the assays described herein.

As used herein, “treating” or “treat” describes the management and care of a patient for the purpose of combating a disease, condition, or disorder and includes the administration of a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, to alleviate the symptoms or complications of a disease, condition or disorder, or to eliminate the disease, condition or disorder.

A composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, can also be used to prevent a disease, condition or disorder. As used herein, “preventing” or “prevent” describes reducing or eliminating the onset of the symptoms or complications of the disease, condition or disorder.

As used herein, the term “alleviate” is meant to describe a process by which the severity of a sign or symptom of a disorder is decreased. Importantly, a sign or symptom can be alleviated without being eliminated. In a preferred embodiment, the administration of pharmaceutical compositions of the disclosure leads to the elimination of a sign or symptom, however, elimination is not required. Effective dosages are expected to decrease the severity of a sign or symptom. For instance, a sign or symptom of a disorder such as cancer, which can occur in multiple locations, is alleviated if the severity of the cancer is decreased within at least one of multiple locations.

As used herein, the term “severity” is meant to describe the potential of cancer to transform from a precancerous, or benign, state into a malignant state. Alternatively, or in addition, severity is meant to describe a cancer stage, for example, according to the TNM system (accepted by the International Union Against Cancer (UICC) and the American Joint Committee on Cancer (AJCC)) or by other art-recognized methods. Cancer stage refers to the extent or severity of the cancer, based on factors such as the location of the primary tumor, tumor size, number of tumors, and lymph node involvement (spread of cancer into lymph nodes). Alternatively, or in addition, severity is meant to describe the tumor grade by art-recognized methods (see, National Cancer Institute, www.cancer.gov). Tumor grade is a system used to classify cancer cells in terms of how abnormal they look under a microscope and how quickly the tumor is likely to grow and spread. Many factors are considered when determining tumor grade, including the structure and growth pattern of the cells. The specific factors used to determine tumor grade vary with each type of cancer. Severity also describes a histologic grade, also called differentiation, which refers to how much the tumor cells resemble normal cells of the same tissue type (see, National Cancer Institute, www.cancer.gov). Furthermore, severity describes a nuclear grade, which refers to the size and shape of the nucleus in tumor cells and the percentage of tumor cells that are dividing (see, National Cancer Institute, www.cancer.gov).

In another aspect of the disclosure, severity describes the degree to which a tumor has secreted growth factors, degraded the extracellular matrix, become vascularized, lost adhesion to juxtaposed tissues, or metastasized. Moreover, severity describes the number of locations to which a primary tumor has metastasized. Finally, severity includes the difficulty of treating tumors of varying types and locations. For example, inoperable tumors, those cancers which have greater access to multiple body systems (hematological and immunological tumors), and those which are the most resistant to traditional treatments are considered most severe. In these situations, prolonging the life expectancy of the subject and/or reducing pain, decreasing the proportion of cancerous cells or restricting cells to one system, and improving cancer stage/tumor grade/histological grade/nuclear grade are considered alleviating a sign or symptom of the cancer.

As used herein the term “symptom” is defined as an indication of disease, illness, injury, or that something is not right in the body. Symptoms are felt or noticed by the individual experiencing the symptom, but may not easily be noticed by others. Others are defined as non-health-care professionals.

As used herein the term “sign” is also defined as an indication that something is not right in the body. But signs are defined as things that can be seen by a doctor, nurse, or other health care professional.

Cancer is a group of diseases that may cause almost any sign or symptom. The signs and symptoms will depend on where the cancer is, the size of the cancer, and how much it affects the nearby organs or structures. If a cancer spreads (metastasizes), then symptoms may appear in different parts of the body.

The disorder in which EZH2-mediated protein methylation plays a part can be a neurological disease. The compound of this disclosure can thus also be used for treating neurologic diseases such as epilepsy, schizophrenia, bipolar disorder or other psychological and/or psychiatric disorders, neuropathies, skeletal muscle atrophy, and neurodegenerative diseases, e.g., a neurodegenerative disease. Exemplary neurodegenerative diseases include: Alzheimer's, Amyotrophic Lateral Sclerosis (ALS), and Parkinson's disease. Another class of neurodegenerative diseases includes diseases caused at least in part by aggregation of poly-glutamine. Diseases of this class include: Huntington's Diseases, Spinalbulbar Muscular Atrophy (SBMA or Kennedy's Disease) Dentatorubropallidoluysian Atrophy (DRPLA), Spinocerebellar Ataxia 1 (SCA1), Spinocerebellar Ataxia 2 (SCA2), Machado-Joseph Disease (MJD; SCA3), Spinocerebellar Ataxia 6 (SCA6), Spinocerebellar Ataxia 7 (SCA7), and Spinocerebellar Ataxia 12 (SCA12).

Any other disease in which epigenetic methylation, which is mediated by EZH2, plays a role may be treatable or preventable using compositions and methods described herein.

Treating cancer can result in a reduction in size of a tumor. A reduction in size of a tumor may also be referred to as “tumor regression”. Preferably, after treatment, tumor size is reduced by 5% or greater relative to its size prior to treatment; more preferably, tumor size is reduced by 10% or greater; more preferably, reduced by 20% or greater; more preferably, reduced by 30% or greater; more preferably, reduced by 40% or greater; even more preferably, reduced by 50% or greater; and most preferably, reduced by greater than 75% or greater. Size of a tumor may be measured by any reproducible means of measurement. The size of a tumor may be measured as a diameter of the tumor.

Treating cancer can result in a reduction in tumor volume. Preferably, after treatment, tumor volume is reduced by 5% or greater relative to its size prior to treatment; more preferably, tumor volume is reduced by 10% or greater; more preferably, reduced by 20% or greater; more preferably, reduced by 30% or greater; more preferably, reduced by 40% or greater; even more preferably, reduced by 50% or greater; and most preferably, reduced by greater than 75% or greater. Tumor volume may be measured by any reproducible means of measurement.

Treating cancer results in a decrease in number of tumors. Preferably, after treatment, tumor number is reduced by 5% or greater relative to number prior to treatment; more preferably, tumor number is reduced by 10% or greater; more preferably, reduced by 20% or greater; more preferably, reduced by 30% or greater; more preferably, reduced by 40% or greater; even more preferably, reduced by 50% or greater; and most preferably, reduced by greater than 75%. Number of tumors may be measured by any reproducible means of measurement. The number of tumors may be measured by counting tumors visible to the naked eye or at a specified magnification. Preferably, the specified magnification is 2×, 3×, 4×, 5×, 10×, or 50×.

Treating cancer can result in a decrease in number of metastatic lesions in other tissues or organs distant from the primary tumor site. Preferably, after treatment, the number of metastatic lesions is reduced by 5% or greater relative to number prior to treatment; more preferably, the number of metastatic lesions is reduced by 10% or greater; more preferably, reduced by 20% or greater; more preferably, reduced by 30% or greater; more preferably, reduced by 40% or greater; even more preferably, reduced by 50% or greater; and most preferably, reduced by greater than 75%. The number of metastatic lesions may be measured by any reproducible means of measurement. The number of metastatic lesions may be measured by counting metastatic lesions visible to the naked eye or at a specified magnification. Preferably, the specified magnification is 2×, 3×, 4×, 5×, 10×, or 50×.

Treating cancer can result in an increase in average survival time of a population of treated subjects in comparison to a population receiving carrier alone. Preferably, the average survival time is increased by more than 30 days; more preferably, by more than 60 days; more preferably, by more than 90 days; and most preferably, by more than 120 days. An increase in average survival time of a population may be measured by any reproducible means. An increase in average survival time of a population may be measured, for example, by calculating for a population the average length of survival following initiation of treatment with an active compound. An increase in average survival time of a population may also be measured, for example, by calculating for a population the average length of survival following completion of a first round of treatment with an active compound.

Treating cancer can result in an increase in average survival time of a population of treated subjects in comparison to a population of untreated subjects. Preferably, the average survival time is increased by more than 30 days; more preferably, by more than 60 days; more preferably, by more than 90 days; and most preferably, by more than 120 days. An increase in average survival time of a population may be measured by any reproducible means. An increase in average survival time of a population may be measured, for example, by calculating for a population the average length of survival following initiation of treatment with an active compound. An increase in average survival time of a population may also be measured, for example, by calculating for a population the average length of survival following completion of a first round of treatment with an active compound.

Treating cancer can result in increase in average survival time of a population of treated subjects in comparison to a population receiving monotherapy with a drug that is not a compound of the present disclosure, or a pharmaceutically acceptable salt, solvate, analog or derivative thereof. Preferably, the average survival time is increased by more than 30 days; more preferably, by more than 60 days; more preferably, by more than 90 days; and most preferably, by more than 120 days. An increase in average survival time of a population may be measured by any reproducible means. An increase in average survival time of a population may be measured, for example, by calculating for a population the average length of survival following initiation of treatment with an active compound. An increase in average survival time of a population may also be measured, for example, by calculating for a population the average length of survival following completion of a first round of treatment with an active compound.

Treating cancer can result in a decrease in the mortality rate of a population of treated subjects in comparison to a population receiving carrier alone. Treating cancer can result in a decrease in the mortality rate of a population of treated subjects in comparison to an untreated population. Treating cancer can result in a decrease in the mortality rate of a population of treated subjects in comparison to a population receiving monotherapy with a drug that is not a compound of the present disclosure, or a pharmaceutically acceptable salt, solvate, analog or derivative thereof. Preferably, the mortality rate is decreased by more than 2%; more preferably, by more than 5%; more preferably, by more than 10%; and most preferably, by more than 25%. A decrease in the mortality rate of a population of treated subjects may be measured by any reproducible means. A decrease in the mortality rate of a population may be measured, for example, by calculating for a population the average number of disease-related deaths per unit time following initiation of treatment with an active compound. A decrease in the mortality rate of a population may also be measured, for example, by calculating for a population the average number of disease-related deaths per unit time following completion of a first round of treatment with an active compound.

Treating cancer can result in a decrease in tumor growth rate. Preferably, after treatment, tumor growth rate is reduced by at least 5% relative to number prior to treatment; more preferably, tumor growth rate is reduced by at least 10%; more preferably, reduced by at least 20%; more preferably, reduced by at least 30%; more preferably, reduced by at least 40%; more preferably, reduced by at least 50%; even more preferably, reduced by at least 50%; and most preferably, reduced by at least 75%. Tumor growth rate may be measured by any reproducible means of measurement. Tumor growth rate can be measured according to a change in tumor diameter per unit time.

Treating cancer can result in a decrease in tumor regrowth. Preferably, after treatment, tumor regrowth is less than 5%; more preferably, tumor regrowth is less than 10%; more preferably, less than 20%; more preferably, less than 30%; more preferably, less than 40%; more preferably, less than 50%; even more preferably, less than 50%; and most preferably, less than 75%. Tumor regrowth may be measured by any reproducible means of measurement. Tumor regrowth is measured, for example, by measuring an increase in the diameter of a tumor after a prior tumor shrinkage that followed treatment. A decrease in tumor regrowth is indicated by failure of tumors to reoccur after treatment has stopped.

Treating or preventing a cell proliferative disorder can result in a reduction in the rate of cellular proliferation. Preferably, after treatment, the rate of cellular proliferation is reduced by at least 5%; more preferably, by at least 10%; more preferably, by at least 20%; more preferably, by at least 30%; more preferably, by at least 40%; more preferably, by at least 50%; even more preferably, by at least 50%; and most preferably, by at least 75%. The rate of cellular proliferation may be measured by any reproducible means of measurement. The rate of cellular proliferation is measured, for example, by measuring the number of dividing cells in a tissue sample per unit time.

Treating or preventing a cell proliferative disorder can result in a reduction in the proportion of proliferating cells. Preferably, after treatment, the proportion of proliferating cells is reduced by at least 5%; more preferably, by at least 10%; more preferably, by at least 20%; more preferably, by at least 30%; more preferably, by at least 40%; more preferably, by at least 50%; even more preferably, by at least 50%; and most preferably, by at least 75%. The proportion of proliferating cells may be measured by any reproducible means of measurement. Preferably, the proportion of proliferating cells is measured, for example, by quantifying the number of dividing cells relative to the number of nondividing cells in a tissue sample. The proportion of proliferating cells can be equivalent to the mitotic index.

Treating or preventing a cell proliferative disorder can result in a decrease in size of an area or zone of cellular proliferation. Preferably, after treatment, size of an area or zone of cellular proliferation is reduced by at least 5% relative to its size prior to treatment; more preferably, reduced by at least 10%; more preferably, reduced by at least 20%; more preferably, reduced by at least 30%; more preferably, reduced by at least 40%; more preferably, reduced by at least 50%; even more preferably, reduced by at least 50%; and most preferably, reduced by at least 75%. Size of an area or zone of cellular proliferation may be measured by any reproducible means of measurement. The size of an area or zone of cellular proliferation may be measured as a diameter or width of an area or zone of cellular proliferation.

Treating or preventing a cell proliferative disorder can result in a decrease in the number or proportion of cells having an abnormal appearance or morphology. Preferably, after treatment, the number of cells having an abnormal morphology is reduced by at least 5% relative to its size prior to treatment; more preferably, reduced by at least 10%; more preferably, reduced by at least 20%; more preferably, reduced by at least 30%; more preferably, reduced by at least 40%; more preferably, reduced by at least 50%; even more preferably, reduced by at least 50%; and most preferably, reduced by at least 75%. An abnormal cellular appearance or morphology may be measured by any reproducible means of measurement. An abnormal cellular morphology can be measured by microscopy, e.g., using an inverted tissue culture microscope. An abnormal cellular morphology can take the form of nuclear pleiomorphism.

As used herein, the term “selectively” means tending to occur at a higher frequency in one population than in another population. The compared populations can be cell populations. Preferably, a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, acts selectively on a cancer or precancerous cell but not on a normal cell. Preferably, a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, acts selectively to modulate one molecular target (e.g., a target protein methyltransferase) but does not significantly modulate another molecular target (e.g., a non-target protein methyltransferase). The disclosure also provides a method for selectively inhibiting the activity of an enzyme, such as a protein methyltransferase. Preferably, an event occurs selectively in population A relative to population B if it occurs greater than two times more frequently in population A as compared to population B. An event occurs selectively if it occurs greater than five times more frequently in population A. An event occurs selectively if it occurs greater than ten times more frequently in population A; more preferably, greater than fifty times; even more preferably, greater than 100 times; and most preferably, greater than 1000 times more frequently in population A as compared to population B. For example, cell death would be said to occur selectively in cancer cells if it occurred greater than twice as frequently in cancer cells as compared to normal cells.

A composition of the present disclosure, e.g., a composition comprising any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt thereof, and one or more other therapeutic agents, such as prednisone, can modulate the activity of a molecular target (e.g., a target protein methyltransferase). Modulating refers to stimulating or inhibiting an activity of a molecular target. Preferably, a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, modulates the activity of a molecular target if it stimulates or inhibits the activity of the molecular target by at least 2-fold relative to the activity of the molecular target under the same conditions but lacking only the presence of said compound. More preferably, a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, modulates the activity of a molecular target if it stimulates or inhibits the activity of the molecular target by at least 5-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold relative to the activity of the molecular target under the same conditions but lacking only the presence of said compound. The activity of a molecular target may be measured by any reproducible means. The activity of a molecular target may be measured in vitro or in vivo. For example, the activity of a molecular target may be measured in vitro by an enzymatic activity assay or a DNA binding assay, or the activity of a molecular target may be measured in vivo by assaying for expression of a reporter gene.

A composition of the present disclosure does not significantly modulate the activity of a molecular target if the addition of the compound does not stimulate or inhibit the activity of the molecular target by greater than 10% relative to the activity of the molecular target under the same conditions but lacking only the presence of said compound.

As used herein, the term “isozyme selective” means preferential inhibition or stimulation of a first isoform of an enzyme in comparison to a second isoform of an enzyme (e.g., preferential inhibition or stimulation of a protein methyltransferase isozyme alpha in comparison to a protein methyltransferase isozyme beta). Preferably, a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, demonstrates a minimum of a fourfold differential, preferably a tenfold differential, more preferably a fifty fold differential, in the dosage required to achieve a biological effect. Preferably, a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, demonstrates this differential across the range of inhibition, and the differential is exemplified at the IC₅₀, i.e., a 50% inhibition, for a molecular target of interest.

Administering a composition of the present disclosure to a cell or a subject in need thereof can result in modulation (i.e., stimulation or inhibition) of an activity of a protein methyltransferase of interest.

Administering a compound of the present disclosure, e.g., a composition comprising any compound of Formulae (I)-(VIa) or pharmaceutically acceptable salt thereof, and one or more other therapeutic agents, such as prednisone, to a cell or a subject in need thereof results in modulation (i.e., stimulation or inhibition) of an activity of an intracellular target (e.g., substrate). Several intracellular targets can be modulated with the compounds of the present disclosure, including, but not limited to, protein methyltrasferase.

Activating refers to placing a composition of matter (e.g., protein or nucleic acid) in a state suitable for carrying out a desired biological function. A composition of matter capable of being activated also has an unactivated state. An activated composition of matter may have an inhibitory or stimulatory biological function, or both.

Elevation refers to an increase in a desired biological activity of a composition of matter (e.g., a protein or a nucleic acid). Elevation may occur through an increase in concentration of a composition of matter.

As used herein, “a cell cycle checkpoint pathway” refers to a biochemical pathway that is involved in modulation of a cell cycle checkpoint. A cell cycle checkpoint pathway may have stimulatory or inhibitory effects, or both, on one or more functions comprising a cell cycle checkpoint. A cell cycle checkpoint pathway is comprised of at least two compositions of matter, preferably proteins, both of which contribute to modulation of a cell cycle checkpoint. A cell cycle checkpoint pathway may be activated through an activation of one or more members of the cell cycle checkpoint pathway. Preferably, a cell cycle checkpoint pathway is a biochemical signaling pathway.

As used herein, “cell cycle checkpoint regulator” refers to a composition of matter that can function, at least in part, in modulation of a cell cycle checkpoint. A cell cycle checkpoint regulator may have stimulatory or inhibitory effects, or both, on one or more functions comprising a cell cycle checkpoint. A cell cycle checkpoint regulator can be a protein or not a protein.

Treating cancer or a cell proliferative disorder can result in cell death, and preferably, cell death results in a decrease of at least 10% in number of cells in a population. More preferably, cell death means a decrease of at least 20%; more preferably, a decrease of at least 30%; more preferably, a decrease of at least 40%; more preferably, a decrease of at least 50%; most preferably, a decrease of at least 75%. Number of cells in a population may be measured by any reproducible means. A number of cells in a population can be measured by fluorescence activated cell sorting (FACS), immunofluorescence microscopy and light microscopy. Methods of measuring cell death are as shown in Li et al., Proc Natl Acad Sci USA. 100(5): 2674-8, 2003. In an aspect, cell death occurs by apoptosis.

Preferably, an effective amount of a composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, is not significantly cytotoxic to normal cells. A therapeutically effective amount of a compound is not significantly cytotoxic to normal cells if administration of the compound in a therapeutically effective amount does not induce cell death in greater than 10% of normal cells. A therapeutically effective amount of a compound does not significantly affect the viability of normal cells if administration of the compound in a therapeutically effective amount does not induce cell death in greater than 10% of normal cells. In an aspect, cell death occurs by apoptosis.

Contacting a cell with a composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, can induce or activate cell death selectively in cancer cells. Administering to a subject in need thereof a compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, can induce or activate cell death selectively in cancer cells. Contacting a cell with a composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, can induce cell death selectively in one or more cells affected by a cell proliferative disorder. Preferably, administering to a subject in need thereof a composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, induces cell death selectively in one or more cells affected by a cell proliferative disorder.

The present disclosure relates to a method of treating or preventing cancer by administering a composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, to a subject in need thereof, where administration of the composition of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof, results in one or more of the following: prevention of cancer cell proliferation by accumulation of cells in one or more phases of the cell cycle (e.g. G1, G1/S, G2/M), or induction of cell senescence, or promotion of tumor cell differentiation; promotion of cell death in cancer cells via cytotoxicity, necrosis or apoptosis, without a significant amount of cell death in normal cells, antitumor activity in animals with a therapeutic index of at least 2. As used herein, “therapeutic index” is the maximum tolerated dose divided by the efficacious dose.

One skilled in the art may refer to general reference texts for detailed descriptions of known techniques discussed herein or equivalent techniques. These texts include Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Inc. (2005); Sambrook et al., Molecular Cloning, A Laboratory Manual (3^(rd) edition), Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2000); Coligan et al., Current Protocols in Immunology, John Wiley & Sons, N.Y.; Enna et al., Current Protocols in Pharmacology, John Wiley & Sons, N.Y.; Fingl et al., The Pharmacological Basis of Therapeutics (1975), Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 18^(th) edition (1990). These texts can, of course, also be referred to in making or using an aspect of the disclosure.

Example 1

Preclinical data have suggested that small molecule inhibitors for the histone methyltransferase EZH2 represent potential new treatment modalities for Non-Hodgkin lymphomas (NHL) expressing EZH2 change of function mutations. It has been previously reported that selective inhibition of EZH2 results in specific killing of lymphoma cells bearing EZH2 mutations in vitro and in vivo, with minimal effects on non-mutant lymphoma cells [Knutson et al. Nature Chemical Biology 2012¹; Keilhack et al. Blood (ASH Annual Meeting Abstracts) 2012, 120, Abstract 3712²]. Since epigenetic changes have been suggested to be involved in resistance of cancer cells to many anticancer agents, Compound 44 in combination with standard of care agents for NHL, second line therapies or targeted therapies that are being explored in this indication was studied. With continuous exposure to Compound 44, cell-based assays of two different EZH2 mutant cell lines demonstrated combination benefits with all components of the CHOP chemotherapy regime, second line therapies but also with several targeted therapies (for instance other epigenetic drugs, PI3K pathway or other inhibitors). These effects were not observed in an EZH2 wild type lymphoma cell line of the activated B cell type. Strong combination benefit with CHOP was also observed in two different EZH2 mutant xenograft models. For instance, in the SUDHL6 Y646N xenograft model neither Compound 44 nor CHOP chemotherapy alone induced a significant antitumor effect, yet their combination produced durable tumor regressions even after cessation of dosing. Importantly, this effect was preserved when doxorubicin was omitted from the CHOP chemotherapy regime in a third study with another EZH2 mutant xenograft model. Subsequently data presented herein showed that glucocorticoid receptor agonism may be a key mechanism of the combination benefit observed with CHOP, as the anti-proliferative effect of Compound 44 was enhanced by either prednisolone or dexamethasone alone, in several EZH2 mutant lymphoma cell lines (in vitro). Taken together these data suggest that the single agent activity of Compound 44 in EZH2 mutant NHL may be further enhanced and expanded through rational combination strategies.

The data presented herein demonstrate that:

Compound 44 and glucocorticoid receptor agonists cooperate to dramatically enhance the antiproliferative activity in EZH2 mutant and wild type GCB lymphoma lines, including EZH2i insensitive mutant lines, but not those of the activated B-cell type in vitro.

In mutant EZH2 GCB lymphoma cells, combination benefit was also observed with all the single components of the CHOP chemotherapy regime, second line and other targeted therapies, including strong synergy with the BCL2 inhibitor, navitoclax and mTOR inhibitor everolimus.

Strong combination benefit with CHOP was observed in two different EZH2 mutant xenograft models, and this effect was preserved in a study in a third EZH2 mutant xenograft model in which doxorubicin was omitted from the chemotherapy regime.

Taken together these results suggest that glucocorticoid receptor agonist may play a key role in the amplified anti-tumor activity observed with combinations of Compound 44 and CHOP in EZH2 mutant lymphoma xenografts and that the observed strong in vitro synergy, with several novel therapies currently evaluated in NHL warrant further investigation of rational combinatorial approaches.

Example 2: Synergistic Anti-Tumor Activity of EZH2 Inhibitors and Glucocorticoid Receptor Agonists in Germinal Center Non-Hodgkin Lymphomas Results

Dramatic synergy was observed when Compound 44 is combined just with the glucocorticoid receptor agonist (GRag) prednisolone of CHOP or with other GRag, such as dexamethasone. When combined with CHOP, the antiproliferative effects of Compound 44 are greatly enhanced and most of this synergy can be ascribed to the GRag component of CHOP, prednisolone (the active metabolite of prednisone). Remarkably, the combination of Compound 44 and prednisolone extends the range of cells that are sensitive to EZH2 inhibition, from mutant-bearing only to all GCB NHL cells.

Two EZH2 mutant cell lines, WSU-DLCL2 and SU-DHL10, were pre-treated with Compound 44 for 4 days and then co-treated with the combination of Compound 44 plus individual CHOP components for 3 additional days (4+3 model). Mafosfamide (an analog of cyclophosphamide), doxorubicin, and vincristine, all showed concentration-dependent growth inhibition in the mutant cell lines by themselves. Hence, combination indices (CI, calculated using Calcusyn software) were obtained for these drugs in combination with Compound 44. These cell lines, however, showed no sensitivity to prednisolone (the active metabolite of prednisone) by itself. Thus, in this case a CI could not be determined and instead an enhancement of potency was calculated based on the shift in IC₅₀ of Compound 44 seen with a concentration-response curve of prednisolone.

The combination of Compound 44+mafosfamide led to an overall additive combination benefit in both EZH2 mutant cell lines (FIGS. 3C and 3F). In WSU-DLCL2 cells, Compound 44+doxorubicin acted synergistically in the 4+3 model (FIG. 3A), while this combination was additive in SU-DHL10 cells (FIG. 3D). The combination of Compound 44+vincristine also demonstrated additivity in both EZH2 mutant cell lines (FIGS. 3B and 3E). When WSU-DLCL2 cells were treated with prednisolone+ Compound 44, a 9-fold shift to greater potency was observed for Compound 44. Treatment with a different GRag, dexamethasone, resulted in an even greater shift in the IC₅₀ of Compound 44 of 17-fold (FIGS. 4A and 4B). A similar trend in potency shift for Compound 44 was observed in SU-DHL10 cells (FIGS. 4C and 4D).

Whether the combination effect of Compound 44+CHOP could render WT EZH2 lymphoma cell lines, both of the GCB and ABC subtype, sensitive to Compound 44 was investigated next. Since Compound 44 treatment alone does not induce growth inhibition in EZH2 WT lymphoma lines, shifts in potency were calculated based on the concentration-response curves of the individual CHOP components. Of the four CHOP components tested, only the combination of GRag+ Compound 44 led to a potency shift in a WT GCB lymphoma cell line (FIGS. 5A and 5B and Table 3). In contrast, no potency shift was observed in a WT ABC lymphoma line with any of the 4 CHOP components (FIGS. 5C and 5D and Table 3), suggesting that the GRag+EZH2i combination benefit is specific to the biology of the GCB subtype of lymphoma.

Given that only the GRag+EZH2i combination induced dramatically enhanced antiproliferative effects, compared to either single agent, in EZH2 WT and mutant GCB lymphoma cell lines, whether duration of treatment and/or sequence of addition of compounds affected sensitivity was determined. The cell line panel was also extended to include two EZH2 WT, two EZH2 mutant, Compound 44 sensitive, and two EZH2 mutant, Compound 44 insensitive cell lines (previously reported by McCabe et al, and unpublished internal data). In the previous 4+3 model, the potency shift was based on either Compound 44 (in EZH2 Y646 sensitive cell lines) or prednisolone (in EZH2 WT cell lines) exposure. For this set of experiments, the Compound 44 IC₅₀ shift at a fixed concentration of prednisolone was used to determine the combination benefit in cell lines treated with either the 4+3 model, 4 day or 7 day co-treatment, or 4 day prednisolone pre-treatment plus 3 days of co-treatment. When EZH2 mutant, Compound 44 sensitive cell lines were co-treated for 4 days, a 30-60 fold lower IC₅₀ of Compound 44 was observed, demonstrating similar trends to that of the 4+3 treatment schedule (Table 2). Similar results were observed with 7 day co-treatment, and the 4+3 model (Table 2). In EZH2 WT GCB cell lines, despite yielding no measureable Compound 44 IC₅₀ after 4 days, both cell lines exhibited decreased proliferation and a measurable Compound 44 IC₅₀ after 4 days of co-treatment with prednisolone (Table 2). EZH2 WT GCB cells also responded to the 4+3 model and/or 7 day co-treatment schedules (Table 2). Strikingly, EZH2 mutant, Compound 44 insensitive cell lines, which also exhibit no measurable Compound 44 IC₅₀ after 4 day treatment, demonstrated decreased proliferation with 4 day co-treatment, with even greater response to the combination with the 4+3 treatment schedule as well as with 7 day co-treatment (Table 2). Only 1 of the 6 cell lines demonstrated a combination benefit when cells were pre-treated with prednisolone, then co-treated with Compound 44+prednisolone, suggesting that the order of drug addition is important for the synergy effect (Table 2). Table 2. Compound 44/GRag Combination Increases EZH2i Sensitivity in EZH2 Y646 Cell Lines and Overcomes EZH2i Insensitivity in Cell Lines Resistant to EZH2i

4 Day Cpd44 IC₅₀ (uM) 7 Day Cpd44 IC₅₀ (uM) Cpd44 Cpd44 4 d Cpd44 Pre/ 4 d Pred Pre/ 7 d Cell Line Alone Co-treatment 3 d Co-treat 3 d Co-treat Co-treatment WSU 0.53 +/− 0.014 0.020 +/− 0.021  0.011 +/− 0.0062 >1 0.014 +/− 0.0049 (Y646-Sens) SU-DHL10 0.64 +/− 0.26  0.0092 +/− 0.0044 0.0027 +/− 0.0013 0.52, >1 0.020 +/− 0.0057 (Y646-Sens) RL >1 0.0096 +/− 0.0066 <<0.004 0.38 <0.004 (Y646-Res) SU-DHL4 >1 >1, 0.2, >1 0.035 +/− 0.043 >1  0.51 +/− 0.35  (Y646-Res) DOHH2 >1 0.20 +/− 0.25 >1, 0.03, >1 >1 0.34 +/− 0.078 (WT) OCI-Ly19 >1 0.19 +/− 0.11 0.0055 +/− 0.0047 >1 0.026, <0.004 (WT)

To investigate the mechanism of action through which this combination benefit of Compound 44+GRag acts in these cell lines, global methylation and acetylation of the histone H3 lysine 27 (H3K27) residue was analyzed. WSU-DLCL2, OCI-LY19, and RL cells were treated with either Compound 44, prednisolone, or their combination for 4 days, and H3K27 modifications were assessed by ELISA or western blot. Prednisolone alone did not have any effect on H3K27 trimethylation (H3K27me3) in either WSU-DCL2 or RL cells, but did result in a modest increase of H3K27me3 at higher doses in OCI-LY19 cells. The combination of Compound 44+prednisolone did not shift the Compound 44 IC₅₀ for H3K27me3 inhibition in any cell line (FIG. 11A). Similarly, H3K27 acetylation levels were not globally affected by prednisolone alone or the combination of Compound 44+prednisolone (FIG. 11B).

Having found that global levels of H3K27 acetylation or trimethylation were unaffected, transcriptional regulation of GR signaling pathways was studied. WSU-DLCL2, SU-DHL10, RL, SU-DHL4, OCI-LY19, and DOHH2 cells were treated with a single concentration of Compound 44, prednisolone, or the combination for 4 days, and gene expression was analyzed using a glucocorticoid signaling PCR array (Table 4). Overall, a larger number of genes were down-regulated with both prednisolone and combination treatments in all cell lines, pointing to a role of GR as both activator and repressor of gene expression. Here, the activating function of GR was focused on and 3 genes which have a synergistic up-regulation in the panel of cell lines with combination treatment were described. Sestrin, a putative tumor suppressor that inhibits mTOR signaling (ref), was identified as a gene commonly up-regulated among the 4 EZH2 mutant cell lines in a synergistic manner with combination treatment, but not in EZH2 WT cell lines (FIG. 10A). TNF expression was synergistically up-regulated only in the EZH2 mutant, Compound 44 insensitive cell lines (FIG. 10B), and TSC22D3/GILZ, while up-regulated in all cell lines by prednisolone, is only synergistically enhanced by combination treatment in EZH2 mutant, Compound 44 sensitive cell lines (FIG. 10C).

TABLE 3 Summary of Combinations with Compound 44 WSU-DLCL2 SU-DHL10 Toledo DOHH2 (EZH2 mutant GCB) (EZH2 mutant GCB) (WT EZH2 ABC) (WT EZH2 GCB) Standard of Prednisolone potency enhanced 7x potency enhanced 3x no effect potency enhanced 2x Care Doxurubicin synergy additive no effect no effect DLBCL Mafosfamide additive additive no effect no effect Vincristine additive additive no effect no effect Other Dexamethasone potency enhanced potency enhanced 5x no effect potency enhanced 4x Therapies 15x no effect = No change in drug IC₅₀ upon addition of EPZ-6438

CI <1 synergy CI = 1 additive CI >1 antagonism

Finally, tumor growth inhibition was assessed in 3 different EZH2 mutant lymphoma xenograft models. SCID or nude mice bearing subcutaneous lymphoma xenografts were co-dosed with Compound 44 and chemotherapy, either CHOP or COP (CHOP without doxorubicin), and compared to single agent treatments. In WSU-DLCL2 xenograft bearing mice, tumor growth inhibition was achieved at all Compound 44 doses and schedules employed, and was better than CHOP chemotherapy alone (FIG. 9A). Moreover, the combination therapy of Compound 44 and CHOP induced a robust anti-tumor response and significantly (p<0.001) better tumor growth inhibition (93%) than with either single agent alone (45% and 71%, for CHOP and Compound 44, respectively). All single treatments were tolerated; there was minor body weight loss (11.3%) in the Compound 44/CHOP combo group after the first cycle after which the mice recovered before the next cycle of treatment.

In a SU-DHL6 xenograft model, significant tumor growth inhibition was not observed with CHOP alone, nor with Compound 44 (FIG. 9B, top panel), in contrast to results previously published by Beguelin et al. using the EZH2 inhibitor GSK503. Strikingly, the combination of Compound 44/CHOP resulted in tumor regression. When dosing was stopped at day 28 and mice were observed out to day 60 for tumor growth delay, this combination resulted in tumor free survival in 58% of the mice (FIG. 9B, bottom panel).

The doxorubicin component of CHOP has a lifetime cumulative dosing limit of <550 mg/m² due to its cardiotoxicity. Therefore, the combination benefit of a Compound 44/chemotherapy regimen that eliminated this component was investigated. In a third study, SU-DHL10 xenograft bearing mice were treated for 28 days with either increasing doses of Compound 44 (BID), doxorubicin-free chemotherapy regimen (COP), or a combination of COP and Compound 44 Tumor growth inhibition was observed at all Compound 44 doses as well as with COP (FIG. 9C, top panel). The 266 mg/kg, 532 mg/kg and COP/Compound 44 combination treatments resulted in regressions that were statistically different from vehicle (p>0.001) as assessed by repeated measures ANOVA and Dunnett's post test, with the Compound 44/COP combination group demonstrating the best overall response. After the 28 day dosing, a sub-group of mice with the smallest tumor burden (8 mice per group) were kept alive without further dosing for a tumor growth delay endpoint. There was a clear dose dependent tumor growth delay benefit for mice treated with Compound 44, while COP treated tumors progressed faster than those treated with Compound 44 (FIG. 9C, middle panel). While mice treated with the maximal tolerated dose of Compound 44 or with the Compound 44/COP combination showed 100% survival on Day 60, the combination group showed the smallest terminal tumor weights, statistically different (p>0.05) from all other treatment groups, including the maximal tolerated dose for Compound 44 (FIG. 9C, bottom panel).

Standard treatments for B-cell NHL are combination chemotherapy regimens composed of cyclophosphamide, doxorubicin, vincristine and prednisolone. While complete response rates of 40-50% can be achieved, a substantial proportion of patients relapse, with 3-year overall survival rates of only about 30%. Relapsed lymphomas can exhibit resistance to a wide range of anticancer drugs, which poses a severe challenge in the clinic to manage these aggressive malignancies. Acquisition of drug resistance in lymphoma is partly driven by the genetic heterogeneity and instability of the tumor cells. Successful treatment of chemoresistant NHL will thus require rational combinations of drugs targeting multiple pathways specific to the different subtypes of B-cell NHL. For instance, in lymphomas of the activated B cell type, constitutive activation of the NFkB pathway has been implicated in therapy resistance, and several novel targeted therapies have shown promise in this subtype.

Epigenetic effectors, such as polycomb, have also been implicated in cancer cell chemo-resistance. EZH2, the catalytic subunit of polycomb repressive complex 2 (PRC2) is a critical oncogenic driver in germinal center derived B-cell lymphomas. These more primitive B-cell malignancies, especially variants expressing EZH2 mutants with altered catalytic activity, require EZH2 for proliferation and survival. Results from preclinical studies forecast great promise for EZH2 catalytic inhibitors for the treatment of such genetically defined cancers, and EZH2 inhibitors may also mitigate chemotherapy resistance. The data presented herein show that Compound 44, a clinical stage EZH2 inhibitor, shows various degrees of combination benefit, ranging from additivity to synergy, with the components of CHOP. Those combination effects were specifically found in lymphomas of the germinal center origin, and, in the case of cyclophosphamide, doxorubicin and vincristine, were restricted to EZH2 mutant-bearing cells. Significant synergy in lymphoma cell killing was also found when Compound 44 was co-dosed with CHOP in vivo. This was especially true in the SU-DHL6 xenograft model where neither single agent showed any significant antitumor actvity, but the combination induced durable regressions in >50% of mice. This reiterates the potential importance of overactive EZH2 in chemoresistance of EZH2 mutant lymphoma. Among the CHOP components, Compound 44 combinations with prednisone induced the strongest antiproliferative activity, and this combination could also render insensitive GCB lymphoma cell lines sensitive to EZH2 inhibition, regardless of the EZH2 mutational status. Additionally, this combination benefit is more apparent when Compound 44 and prednisolone are either dosed together or in a sequence specific manner; thus, priming cells with an EZH2 inhibitor, followed by treatment with GR agonists proved particularly effective. This surprising finding has potentially important implications for the application of EZH2 inhibitors in the clinic. First, the widely used GRag are frequently co-administrated with anticancer drugs to prevent drug-induced allergic reactions and to relieve pain, nausea, and emesis, and are pivotal in the treatment of hematopoietic malignancies owing to their ability to induce apoptosis in these cancers. Compared to the other CHOP components, GRag induces the least severe adverse effects. Further, the opportunity to eliminate doxorubicin from the CHOP regime while preserving a combination benefit with Compound 44, as suggested by the data in the SU-DHL10 xenograft model, could spare patients from the dose-limiting cardiotoxic side effects of doxorubicin. Finally, preclinical studies have shown that single agent EZH2 inhibitors induce significant cell killing only in EZH2 mutant-bearing lymphomas, which represent a fraction (20%) of GCB lymphoma patients with high unmet clinical need. The results here demonstrate that GRag/EZH2 inhibitor combinations may have clinical utility in all germinal center derived B cell lymphomas.

Glucocorticoid bound GR molecules move to the nucleus and can act as either transcriptional activator or repressor, depending on the cellular environment. It has been suggested that GR constantly samples the nucleosome for a productive interaction, and the purpose of chromatin-modifying enzymes is to provide regulated access of GR, its cofactors and the basal transcription machinery to DNA. Other studies show that GR often binds to preexisting regions of open chromatin, and the chromatin architecture in a given cell type is organized such that GR can act in a tissue specific manner. Accessibility to GR binding sites can further be enhanced by ATP-dependent chromatin remodeling, and the SWI/SNF complex plays a key role in this activity. Not wishing to be bound by a particular theory or a specific mechanism of action, it is conceivable that aberrant chromatin repression, induced by EZH2 mediated hypertrimethylation of H3K27, can block some of the otherwise accessible GR binding sites, interfering with normal GR mediated gene induction or repression. Indeed, all EZH2 mutant lymphoma cell lines are insensitive to GRag treatment, while concentration-dependent cell killing is observed in EZH2 WT cells. The observation that pretreatment with prednisolone, followed by Compound 44 treatment, cannot induce synergy in almost all cell lines tested, points towards the possibility of EZH2 inhibitor induced chromatin remodeling being the rate limiting step for the enhanced action of GR. Also, PRC2 is known to antagonize with SWI/SNF function and the down-regulation of core subunits of the SWI/SNF complex—SMARCA4, ARIDIA, and INI1—have been associated with resistance to prednisolone in acute lymphoblastic T-cell leukemia. Since the relationship of INI1 loss and EZH2 over-activation has been established in rhabdoid tumors, whether global INI1 protein levels would increase in various lymphoma cells exposed to Compound 44 or prednisolone, potentially allowing greater accessibility of GR to its binding sites after increased SWI/SNF function, was investigated.

GR pathway gene expression arrays revealed both increased and decreased gene expression after treatment of several GCB lymphoma cells (both EZH2 WT and mutant) with either Compound 44, prednisolone or their combination, confirming the dual function of GR. The only gene that was synergistically up-regulated with the combination in all EZH2 mutant lymphoma cells was SESN1, a TP53 tumor suppressor with functions in cellular response to DNA damage and oxidative stress. Sestrins inhibit cell growth by activating AMP-activated protein kinase, resulting in the inhibition of the mTOR pathway. Hence SESN1 mediated mTOR pathway inhibition may be an important mechanism of reintroducing GRag sensitivity in EZH2 mutant lymphoma cells after Compound 44 treatment.

Conversely, GRag/Compound 44 combination treatment could also induce cell killing in those EZH2 mutant lymphoma cell lines that have been reported as refractory to EZH2 inhibitor treatment (RL, SU-DHL4). SESN1 was induced with combination treatment in those cell lines as well, but an additional synergistic up-regulation of TNF, a potent inflammatory cytokine, was observed specifically in RL and SU-DHL4 cells. This observation seems surprising as TNF and glucocorticoids usually act antagonistically. TNF, through its receptor TNFR-1, can induce apoptosis, but also has the ability to transduce survival signals, mainly through the NFkB pathway. It is thus possible that increased TNF expression, induced by the Compound 44/prednisolone combination, may shift TNF action towards apoptosis in the context of GR agonist repression of NFkB-mediated transcription. It is unclear, however, why this mechanism would result in synergistic cell killing in Compound 44 insensitive EZH2 mutant cells. The potential importance of aberrant repression of negative regulators of the NFkB pathway in GRag resistance and the potential role of EZH2 mediating that is further supported by the observation that GILZ is synergistically up-regulated in 2 out of 6 cells lines with the combination.

Methods Medium Throughput Assay

Lymphoma cells were seeded into flasks (50,000 cells/mL for WSU-DLCL2 and DOHH2, 10,000 cells/mL for SU-DHL10, and 100,000 cells/mL for Toledo) and pretreated with 7 doses of Compound 44 or DMSO for 4 days or 6 days for Toledo assays. Cells were then split back to 50,000 cells/mL for WSU-DLCL2 and DOHH2 or 30,000 cells/mL for SU-DHL-10 and co-treated with Compound 44 and compound of interest using the HP D300 digital dispenser (Tecan). Both drugs were serially diluted two-fold and combined in a matrix with constant ratios diagonally across the plate with a final DMSO content of 0.11% (v/v). After 3 days of co-treatment (5 days for Toledo assays), cell viability was measured via ATP content using CellTiter-Glo® (Promega) and luminescence was detected using a SpectraMax M5 microplate reader (Molecular Devices).

Synergy quantification is performed using the Chou-Talalay method for drug combination (Ref 1). The Combination Index (CI) equation offers a quantitative definition for additivity (CI=1), synergism (CI<1), and antagonism (CI>1). This equation used fractional effect (Fa) values from a constant ratio of drug combination to determine CI values. The resulting plot (Fa-CI) plot shows the resultant CI values bracketed by 95% confidence intervals. These Fa-CI plots are generated using the Calcusyn for Windows software (Ref 2). CI values <1 with confidence interval lines also below 1 indicate statistically significant synergism.

For drug combinations where only one drug showed more than 50% inhibition, Potency shifts were determined. Dose responses were plotted using Graphpad Prism and either 50% or 60% inhibitory concentrations were interpolated from the dose response curves. Potency shifts were considered significant when confidence intervals for dose responses did not overlap.

Cell Lines, Compounds, and Treatment Outline

WSU-DLCL2, SU-DHL10, RL, SU-DHL4, OCI-Lyl9, and DOHH2 were previously described (NatChemBio 2012). For combination studies, a modified version of the proliferation assay in suspension cells was used, as previously described (Daigle et al). Briefly, on day 0, cells were plated in triplicate in 96-well plates at initial densities to ensure linear log phase growth over 4 days. Cells were treated with either a dose curve of Compound 44 (starting at a top dose of 1 μM), a single dose of prednisolone (Catalog # and Manufacturer) at a concentration 10-fold lower than the 4-day IC50 of the drug, or a combination of Compound 44+prednisolone. On day 4, cells were counted using Viacount reagent in the guava easyCyte flow cytometer, and the viable cell number was used to replate cells at the original densities for 3 additional days. Cells that were pre-treated with Compound 44 either received continuous Compound 44 alone, or Compound 44+prednisolone (constant dose); cells pre-treated with prednisolone either received continuous prednisolone, or prednisolone+ Compound 44; cells co-treated for 4 days continued to receive co-treatment through 7 days.

Xenograft Studies

All the procedures related to animal handling, care and the treatment in this study were performed according to the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of CRL Piedmont and Shanghai ChemPartner following the guidance of the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). WSU-DLCL2, SU-DHL6, or SU-DHL10 cells were harvested during mid-log phase growth, and re-suspended in PBS with 50% Matrigel™ (BD Biosciences), and injected into immune-compromised mice. Each mouse received 1×107 cells (0.2 mL cell suspension) subcutaneously in the right flank, and once tumors reached a predetermined size, mice were orally dosed with different doses of Compound 44 at various schedules for up to 28 days and/or CHOP/COP on the following schedules: Cyclophosphamide was administered intraperitoneally (i.p.), and doxorubicin and vincristine were each administered via bolus tail vein injections (i.v.); each was given once daily on Days 1 and 8 in the SU-DHL6 study, and on Days 1 and 22 in the WSU-DLCL2 and SU-DHL10 studies. Prednisone was administered p.o. on two cycles of five daily doses, starting on Days 1 and 8 ((qd×5)×2, Days 1, 8) in the SU-DHL6 study, and on Days 1 and 22 ((qd×5)×2, Days 1, 22) in the WSU-DLCL2 and SU-DHL10 studies. Each dose was delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals. Tumor measurements and body weights were collected twice-weekly for 28 days for all studies. To determine tumor growth delay in the SU-DHL10 and SU-DHL6 studies, each test animal was euthanized when its neoplasm reached the endpoint volume of 2000 mm3 or on the last day of the study (day 60), whichever came first.

Quantitative PCR

WSU-DLCL2, SU-DHL10, RL, SU-DHL4, OCI-LY19, and DOHH2 cells were treated in parallel with DMSO, 1 uM of Compound 44 (SU-DHL10 treated with 100 nM Compound 44), a dose of prednisolone at a concentration 10-fold lower than the 4-day IC₅₀, or the combination of drugs for 4 days. Cells were harvested and total mRNA was extracted from cell pellets using the RNeasy Plus Mini Kit (Qiagen; 74134). For the RT2 Glucocorticoid Signaling PCR array (Qiagen; PAHS-154ZE-4), cDNA was made by RT2 First Strand Kit (Qiagen; 330401). Array RT-PCR was performed using ViiA 7 Real-Time PCR Systems [Applied Biosystems (AB)] with RT2 SYBR Green ROX qPCR Mastermix (Qiagen; 330521). Gene expression was normalized to array's B2M and fold change compared to DMSO was calculated using the AACt method. To validate array data, TaqMan probe based qPCR was carried out using TaqMan Fast Advanced Master Mix (AB; 4444964) and TaqMan primer/probe sets for Sestrin (AB; Hs00902787_m1) and TNF (AB; Hs01113624_m1). Fold change was calculated as above, normalizing to RPLPO (AB; 4333761F).

ELISA

Histones were extracted from tumor samples as described above. Histones were prepared in equivalent concentrations in coating buffer (PBS+0.05% BSA) yielding 0.5 ng/ul of sample, and 100 ul of sample or standard was added in duplicate to 2 96-well ELISA plates (Thermo Labsystems, Immulon 4HBX #3885). The plates were sealed and incubated overnight at 4° C. The following day, plates were washed 3× with 300 ul/well PBST (PBS+0.05% Tween 20; 10×PBST, KPL #51-14-02) on a Bio Tek plate washer. Plates were blocked with 300 ul/well of diluent (PBS+2% BSA+0.05% Tween 20), incubated at RT for 2 hours, and washed 3× with PBST. All antibodies were diluted in diluent. 100 ul/well of anti-H3K27me3 (CST #9733, 50% glycerol stock 1:1,000) or anti-total H3 (Abcam ab1791, 50% glycerol 1:10,000) was added to each plate. Plates were incubated for 90 min at RT and washed 3× with PBST. 100 ul/well of anti-R_(b)-IgG-HRP (Cell Signaling Technology, 7074) was added 1:2,000 to the H3K27Me3 plate and 1:6,000 to the H3 plate and incubated for 90 min at RT. Plates were washed 4× with PBST. For detection, 100 ul/well of TMB substrate (BioFx Laboratories, # TMBS) was added and plates incubated in the dark at RT for 5 min. Reaction was stopped with 100 ul/well 1N H₂SO₄. Absorbance at 450 nm was read on SpectaMax M5 Microplate reader.

TABLE 4a Ct values and fold changes from the RT2 Glucocorticoid signaling PCR array analysis for OCI cell line. Ct Values ΔCT (B2M) Gene DMSO Cpd44 Pred Combo DMSO Cpd44 Pred Combo ADARB1 24.373 23.799 24.946 24.323 7.368 6.580 7.319 7.177 AFF1 21.574 21.780 21.892 21.613 4.569 4.561 4.265 4.467 AK2 20.300 20.497 20.859 20.656 3.295 3.278 3.232 3.510 AMPD3 27.424 26.984 27.937 27.892 10.419 9.765 10.310 10.746 ANGPTL4 30.465 30.374 30.333 29.769 13.460 13.155 12.706 12.623 ANXA4 23.319 23.379 24.130 23.394 6.314 6.160 6.503 6.248 AQP1 Undetermined 31.992 Undetermined Undetermined N/A 14.773 N/A N/A ARID5B 22.092 22.537 22.635 22.538 5.087 5.318 5.008 5.392 ASPH 27.926 27.556 28.894 27.701 10.921 10.337 11.267 10.555 ATF4 18.500 18.838 19.578 19.368 1.495 1.619 1.951 2.222 BCL6 27.421 26.240 28.282 26.459 10.416 9.021 10.655 9.313 BMPER Undetermined 34.674 Undetermined 32.290 N/A 17.455 N/A 15.144 CALCR Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CEBPA 30.199 27.522 30.852 28.731 13.194 10.303 13.225 11.585 CEBPB 23.119 23.723 24.427 24.678 6.114 6.504 6.800 7.532 COL4A2 32.777 33.300 35.000 32.293 15.772 16.081 17.373 15.147 CREB1 22.477 22.697 23.159 22.702 5.472 5.478 5.532 5.556 CREB3 24.708 24.979 25.174 24.863 7.703 7.760 7.547 7.717 CREB3L4 24.162 24.000 24.936 24.497 7.157 6.781 7.309 7.351 CTGF 21.557 21.719 21.099 20.311 4.552 4.500 3.472 3.165 CYB561 Undetermined 33.134 Undetermined 32.534 N/A 15.915 N/A 15.388 DDIT4 24.102 23.567 23.551 23.195 7.097 6.348 5.924 6.049 DIRAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A DUSP1 20.981 20.800 21.767 21.200 3.976 3.581 4.140 4.054 EDN1 Undetermined Undetermined 33.433 32.487 N/A N/A 15.806 15.341 EHD3 28.984 28.117 28.833 27.236 11.979 10.898 11.206 10.090 ERRFI1 Undetermined Undetermined 32.824 Undetermined N/A N/A 15.197 N/A FKBP5 22.604 22.499 22.353 21.699 5.599 5.280 4.726 4.553 FOSL2 26.226 26.214 26.368 25.547 9.221 8.995 8.741 8.401 GDPD1 26.444 26.638 27.196 26.808 9.439 9.419 9.569 9.662 GHRHR 37.467 33.641 35.486 36.113 20.462 16.422 17.859 18.967 GLUL 22.916 22.385 23.448 22.402 5.911 5.166 5.821 5.256 GOT1 23.094 23.224 23.810 23.450 6.089 6.005 6.183 6.304 H6PD 26.842 26.141 26.981 26.440 9.837 8.922 9.354 9.294 HAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A HNRPLL 29.840 29.708 30.306 29.439 12.835 12.489 12.679 12.293 IL10 Undetermined Undetermined 34.155 Undetermined N/A N/A 16.528 N/A IL1RN 33.932 32.902 Undetermined Undetermined 16.927 15.683 N/A N/A IL6 Undetermined Undetermined Undetermined 32.602 N/A N/A N/A 15.456 IL6R Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A KLF13 23.416 23.178 23.963 23.145 6.411 5.959 6.336 5.999 KLF9 29.546 28.545 28.597 27.791 12.541 11.326 10.970 10.546 LOX 33.344 32.825 32.787 31.904 16.339 15.606 15.160 14.758 MERTK 29.340 28.749 29.685 28.885 12.335 11.530 12.058 11.739 MT1E Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A MT2A 22.845 22.941 23.298 22.515 5.840 5.722 5.671 5.369 NFKBIA 21.672 21.905 22.337 21.755 4.667 4.686 4.710 4.609 NR3C1 20.940 21.131 21.276 20.605 3.935 3.912 3.649 3.459 PDCD7 23.121 23.359 28.314 23.491 6.116 6.140 10.687 6.345 PDGFRB 32.160 33.308 30.540 30.932 15.155 16.089 12.913 13.786 PDP1 26.092 25.788 26.292 25.520 9.087 8.569 8.665 8.374 PER1 24.615 25.503 25.500 26.016 7.610 8.284 7.873 8.870 PER2 Undetermined 23.177 23.707 23.482 N/A 5.958 6.080 6.336 PIK3R1 23.175 23.115 23.678 23.317 6.170 5.896 6.051 6.171 PLD1 Undetermined Undetermined Undetermined 33.540 N/A N/A N/A 16.394 PLEKHF1 30.216 29.694 30.977 30.285 13.211 12.475 13.350 13.139 POU2F1 24.562 24.656 25.232 24.555 7.557 7.437 7.605 7.409 POU2F2 31.495 31.740 31.543 31.643 14.490 14.521 13.916 14.497 RASA3 23.112 23.251 23.743 23.462 6.107 6.032 6.115 6.316 RGS2 28.455 27.701 29.467 28.122 11.450 10.482 11.840 10.976 RHOB 22.108 20.944 20.967 19.659 5.103 3.725 3.340 2.513 RHOJ Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A SESN1 22.463 22.424 23.126 22.491 5.458 5.205 5.499 5.345 SGK1 26.351 26.107 25.819 24.816 9.346 8.888 8.192 7.670 SLC10A6 31.403 30.432 31.656 32.746 14.398 13.213 14.029 15.600 SLC19A2 24.878 24.881 25.910 25.274 7.873 7.662 8.283 8.128 SLC22A5 29.254 29.101 30.112 29.115 12.249 11.882 12.485 11.969 SNTA1 28.151 27.457 28.892 28.483 11.146 10.238 11.265 11.337 SPHK1 28.555 28.787 29.199 29.124 11.550 11.568 11.572 11.978 SPSB1 27.338 27.455 28.347 28.097 10.333 10.236 10.720 10.951 STAT5A 22.115 22.442 22.673 22.391 5.110 5.223 5.046 5.245 STAT5B 22.886 22.979 23.838 23.297 5.881 5.760 6.211 6.151 TBL1XR1 21.317 21.488 21.705 21.430 4.312 4.269 4.078 4.284 TNF 24.763 24.377 24.612 23.620 7.758 7.158 6.985 6.474 TNFAIP3 22.296 22.827 23.168 23.327 5.291 5.608 5.541 6.181 TSC22D3 25.692 25.235 24.619 24.219 8.687 8.016 6.992 7.073 USP2 33.949 31.341 33.986 32.493 16.944 14.122 16.359 15.347 USP54 24.856 25.235 25.764 24.989 7.851 8.016 8.137 7.843 VDR 25.093 24.754 24.985 24.651 8.088 7.535 7.358 7.505 VLDLR 28.968 28.902 29.671 29.488 11.963 11.683 12.044 12.342 XDH Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A ZFP36 24.550 25.191 Undetermined 25.349 7.545 7.972 N/A 8.203 ZHX3 24.941 24.761 24.833 24.322 7.936 7.542 7.206 7.176 ZNF281 22.504 23.249 23.997 23.695 5.499 6.030 6.370 6.549 ACTB 15.098 14.892 16.093 14.987 −1.907 −2.327 −1.534 −2.159 B2M 17.005 17.219 17.627 17.146 0.000 0.000 0.000 0.000 GAPDH 15.880 16.149 16.519 16.647 −1.125 −1.070 −1.108 −0.499 HPRT1 21.462 21.828 22.125 21.813 4.457 4.609 4.498 4.667 RPLP0 14.351 14.350 15.011 14.197 −2.654 −2.869 −2.616 −2.949 HGDC Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A RTC 22.174 21.961 21.962 22.251 5.169 4.742 4.335 5.105 RTC 22.089 21.953 22.140 22.008 5.084 4.734 4.513 4.862 RTC 22.195 21.961 22.167 21.993 5.190 4.742 4.540 4.847 PPC 18.397 18.268 18.432 18.371 1.392 1.049 0.805 1.225 PPC 18.426 18.330 18.320 18.347 1.421 1.111 0.693 1.201 PPC 18.301 17.672 18.372 18.378 1.296 0.453 0.745 1.232 Cpd44 Pred Combo Gene ΔΔCT Fold Change ΔΔCT Fold Change ΔΔCT Fold Change ADARB1 −0.788 1.727 −0.049 1.035 −0.191 1.142 AFF1 −0.008 1.006 −0.304 1.235 −0.102 1.073 AK2 −0.017 1.012 −0.063 1.045 0.215 0.862 AMPD3 −0.654 1.574 −0.109 1.078 0.327 0.797 ANGPTL4 −0.305 1.235 −0.754 1.686 −0.837 1.786 ANXA4 −0.154 1.113 0.189 0.877 −0.066 1.047 AQP1 N/A N/A N/A N/A N/A N/A ARID5B 0.231 0.852 −0.079 1.056 0.305 0.809 ASPH −0.584 1.499 0.346 0.787 −0.366 1.289 ATF4 0.124 0.918 0.456 0.729 0.727 0.604 BCL6 −1.395 2.630 0.239 0.847 −1.103 2.148 BMPER N/A N/A N/A N/A N/A N/A CALCR N/A N/A N/A N/A N/A N/A CEBPA −2.891 7.418 0.031 0.979 −1.609 3.050 CEBPB 0.390 0.763 0.686 0.622 1.418 0.374 COL4A2 0.309 0.807 1.601 0.330 −0.625 1.542 CREB1 0.006 0.996 0.060 0.959 0.084 0.943 CREB3 0.057 0.961 −0.156 1.114 0.014 0.990 CREB3L4 −0.376 1.298 0.152 0.900 0.194 0.874 CTGF −0.052 1.037 −1.080 2.114 −1.387 2.615 CYB561 N/A N/A N/A N/A N/A N/A DDIT4 −0.749 1.681 −1.173 2.255 −1.048 2.068 DIRAS2 N/A N/A N/A N/A N/A N/A DUSP1 −0.395 1.315 0.164 0.893 0.078 0.947 EDN1 N/A N/A N/A N/A N/A N/A EHD3 −1.081 2.116 −0.773 1.709 −1.889 3.704 ERRFI1 N/A N/A N/A N/A N/A N/A FKBP5 −0.319 1.247 −0.873 1.831 −1.046 2.065 FOSL2 −0.226 1.170 −0.480 1.395 −0.820 1.765 GDPD1 −0.020 1.014 0.130 0.914 0.223 0.857 GHRHR −4.040 16.450  −2.603 6.075 −1.495 2.819 GLUL −0.745 1.675 −0.090 1.064 −0.655 1.575 GOT1 −0.084 1.060 0.094 0.937 0.215 0.862 H6PD −0.915 1.886 −0.483 1.398 −0.543 1.457 HAS2 N/A N/A N/A N/A N/A N/A HNRPLL −0.346 1.271 −0.156 1.114 −0.542 1.456 IL10 N/A N/A N/A N/A N/A N/A IL1RN −1.244 2.369 N/A N/A N/A N/A IL6 N/A N/A N/A N/A N/A N/A IL6R N/A N/A N/A N/A N/A N/A KLF13 −0.452 1.368 −0.075 1.053 −0.412 1.331 KLF9 −1.215 2.321 −1.571 2.971 −1.896 3.722 LOX −0.733 1.662 −1.179 2.264 −1.581 2.992 MERTK −0.805 1.747 −0.277 1.212 −0.596 1.512 MT1E N/A N/A N/A N/A N/A N/A MT2A −0.118 1.085 −0.169 1.124 −0.471 1.386 NFKBIA 0.019 0.987 0.043 0.971 −0.058 1.041 NR3C1 −0.023 1.016 −0.286 1.219 −0.476 1.391 PDCD7 0.024 0.984 4.571 0.042 0.229 0.853 PDGFRB 0.934 0.523 −2.242 4.731 −1.369 2.583 PDP1 −0.518 1.432 −0.422 1.340 −0.713 1.639 PER1 0.674 0.627 0.263 0.833 1.260 0.418 PER2 N/A N/A N/A N/A N/A N/A PIK3R1 −0.274 1.209 −0.119 1.086 0.001 0.999 PLD1 N/A N/A N/A N/A N/A N/A PLEKHF1 −0.736 1.666 0.139 0.908 −0.072 1.051 POU2F1 −0.120 1.087 0.048 0.967 −0.148 1.108 POU2F2 0.031 0.979 −0.574 1.489 0.007 0.995 RASA3 −0.075 1.053 0.009 0.994 0.209 0.865 RGS2 −0.968 1.956 0.390 0.763 −0.474 1.389 RHOB −1.378 2.599 −1.763 3.394 −2.590 6.021 RHOJ N/A N/A N/A N/A N/A N/A SESN1 −0.253 1.192 0.041 0.972 −0.113 1.081 SGK1 −0.458 1.374 −1.154 2.225 −1.676 3.195 SLC10A6 −1.185 2.274 −0.369 1.291 1.202 0.435 SLC19A2 −0.211 1.157 0.410 0.753 0.255 0.838 SLC22A5 −0.367 1.290 0.236 0.849 −0.280 1.214 SNTA1 −0.908 1.876 0.119 0.921 0.191 0.876 SPHK1 0.018 0.988 0.022 0.985 0.428 0.743 SPSB1 −0.097 1.070 0.387 0.765 0.618 0.652 STAT5A 0.113 0.925 −0.064 1.045 0.135 0.911 STAT5B −0.121 1.087 0.330 0.796 0.270 0.829 TBL1XR1 −0.043 1.030 −0.234 1.176 −0.028 1.020 TNF −0.600 1.516 −0.773 1.709 −1.284 2.435 TNFAIP3 0.317 0.803 0.250 0.841 0.890 0.540 TSC22D3 −0.671 1.592 −1.695 3.238 −1.614 3.061 USP2 −2.822 7.071 −0.585 1.500 −1.597 3.025 USP54 0.165 0.892 0.286 0.820 −0.008 1.006 VDR −0.553 1.467 −0.730 1.659 −0.583 1.498 VLDLR −0.280 1.214 0.081 0.945 0.379 0.769 XDH N/A N/A N/A N/A N/A N/A ZFP36 0.427 0.744 N/A N/A 0.658 0.634 ZHX3 −0.394 1.314 −0.730 1.659 −0.760 1.693 ZNF281 0.531 0.692 0.871 0.547 1.050 0.483 ACTB B2M GAPDH HPRT1 RPLP0 HGDC RTC RTC RTC PPC PPC PPC

TABLE 4b Ct values and fold changes from the RT2 Glucocorticoid signaling PCR array analysis for DOHH2 cell line. Ct Values ΔCT (B2M) Gene DMSO Cpd44 Pred Combo DMSO Cpd44 Pred Combo ADARB1 31.818 31.431 33.560 30.189 12.809 12.855 14.676 12.038 AFF1 24.684 23.888 23.992 23.224 5.675 5.312 5.108 5.073 AK2 20.334 20.173 20.262 19.961 1.325 1.597 1.378 1.810 AMPD3 26.401 26.146 27.535 26.852 7.392 7.570 8.651 8.701 ANGPTL4 31.134 30.820 31.538 30.854 12.125 12.244 12.654 12.703 ANXA4 24.817 24.273 24.997 24.268 5.808 5.697 6.113 6.117 AQP1 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A ARID5B 23.881 23.782 23.885 23.886 4.872 5.206 5.001 5.735 ASPH 22.970 22.823 23.369 22.996 3.961 4.247 4.485 4.845 ATF4 19.156 19.190 19.313 18.983 0.147 0.614 0.429 0.832 BCL6 21.529 21.323 21.801 21.773 2.520 2.747 2.917 3.622 BMPER 38.037 39.092 39.378 39.656 19.028 20.516 20.494 21.505 CALCR Undetermined 33.630 Undetermined Undetermined N/A 15.054 N/A N/A CEBPA 34.654 30.676 32.188 30.646 15.645 12.100 13.304 12.495 CEBPB 23.911 23.925 24.317 24.001 4.902 5.349 5.433 5.850 COL4A2 32.314 34.119 38.993 34.143 13.305 15.543 20.109 15.992 CREB1 22.930 22.746 22.890 22.730 3.921 4.170 4.006 4.579 CREB3 24.929 24.840 24.865 24.647 5.920 6.264 5.981 6.496 CREB3L4 24.405 24.110 24.616 24.373 5.396 5.534 5.732 6.222 CTGF 33.711 32.760 33.728 33.696 14.702 14.184 14.844 15.545 CYB561 37.790 31.945 39.582 34.331 18.781 13.369 20.698 16.180 DDIT4 23.934 23.508 24.105 22.948 4.925 4.932 5.221 4.797 DIRAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A DUSP1 27.604 27.132 27.866 27.262 8.595 8.556 8.982 9.111 EDN1 31.233 32.260 32.263 31.224 12.224 13.684 13.379 13.073 EHD3 32.315 28.852 31.098 28.674 13.306 10.276 12.214 10.523 ERRFI1 32.525 30.163 32.635 29.588 13.516 11.587 13.751 11.437 FKBP5 21.985 21.520 20.912 20.512 2.976 2.944 2.028 2.361 FOSL2 31.767 29.872 31.543 29.925 12.758 11.296 12.659 11.774 GDPD1 27.532 27.570 27.884 27.396 8.523 8.994 9.000 9.245 GHRHR 37.684 39.644 36.095 37.813 18.675 21.068 17.211 19.662 GLUL 36.133 36.671 34.574 36.099 17.124 18.095 15.690 17.948 GOT1 23.427 23.126 23.532 22.880 4.418 4.550 4.648 4.729 H6PD 24.717 24.377 24.969 24.453 5.708 5.801 6.085 6.302 HAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A HNRPLL 30.324 29.151 33.284 31.380 11.315 10.575 14.400 13.229 IL10 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A IL1RN Undetermined 32.271 33.560 31.586 N/A 13.695 14.676 13.435 IL6 Undetermined Undetermined 34.758 37.608 N/A N/A 15.874 19.457 IL6R Undetermined 31.962 Undetermined 32.383 N/A 13.386 N/A 14.232 KLF13 22.951 22.420 22.546 21.765 3.942 3.844 3.662 3.614 KLF9 28.691 28.439 28.547 27.741 9.682 9.863 9.663 9.590 LOX 33.562 32.997 34.158 32.855 14.553 14.421 15.274 14.704 MERTK 32.997 32.456 32.892 31.474 13.988 13.880 14.008 13.323 MT1E 39.692 Undetermined Undetermined Undetermined 20.683 N/A N/A N/A MT2A 39.646 Undetermined Undetermined Undetermined 20.637 N/A N/A N/A NFKBIA 22.891 22.625 22.830 22.625 3.882 4.049 3.946 4.474 NR3C1 22.602 22.430 22.794 22.573 3.593 3.854 3.910 4.422 PDCD7 23.656 23.417 23.552 23.397 4.647 4.841 4.668 5.246 PDGFRB Undetermined 35.193 34.934 31.552 N/A 16.617 16.050 13.401 PDP1 25.863 25.175 25.682 25.330 6.854 6.599 6.798 7.179 PER1 24.944 24.717 25.142 25.289 5.935 6.141 6.258 7.138 PER2 24.642 23.835 24.159 23.476 5.633 5.259 5.275 5.325 PIK3R1 24.177 23.712 23.850 23.610 5.168 5.136 4.966 5.459 PLD1 37.038 Undetermined 37.120 38.323 18.029 N/A 18.236 20.172 PLEKHF1 29.886 28.946 29.414 28.738 10.877 10.370 10.530 10.587 POU2F1 24.378 24.003 24.648 23.667 5.369 5.427 5.764 5.516 POU2F2 22.469 22.167 22.489 21.930 3.460 3.591 3.605 3.779 RASA3 27.152 27.636 27.803 28.392 8.143 9.060 8.919 10.241 RGS2 24.790 24.861 25.514 25.639 5.781 6.285 6.630 7.488 RHOB 32.661 30.745 33.162 30.702 13.652 12.169 14.278 12.551 RHOJ Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A SESN1 24.226 23.848 22.839 21.993 5.217 5.272 3.955 3.842 SGK1 27.633 27.821 29.628 29.125 8.624 9.245 10.744 10.974 SLC10A6 34.483 36.435 36.176 32.738 15.474 17.859 17.292 14.587 SLC19A2 25.600 24.859 25.455 24.769 6.591 6.283 6.571 6.618 SLC22A5 28.392 27.992 28.915 27.835 9.383 9.416 10.031 9.684 SNTA1 24.584 24.550 25.124 25.000 5.575 5.974 6.240 6.849 SPHK1 30.677 28.863 29.971 28.646 11.668 10.287 11.087 10.495 SPSB1 27.110 26.652 26.911 26.621 8.101 8.076 8.027 8.470 STAT5A 24.237 23.771 23.885 23.477 5.228 5.195 5.001 5.326 STAT5B 22.503 22.328 22.632 22.414 3.494 3.752 3.748 4.263 TBL1XR1 21.397 20.994 21.304 21.133 2.388 2.418 2.420 2.982 TNF 31.328 31.849 31.956 31.194 12.319 13.273 13.072 13.043 TNFAIP3 28.260 27.520 Undetermined 30.586 9.251 8.944 N/A 12.435 TSC22D3 25.176 24.752 23.310 22.374 6.167 6.176 4.426 4.223 USP2 24.104 23.684 23.501 22.971 5.095 5.108 4.617 4.820 USP54 26.599 25.892 26.683 25.856 7.590 7.316 7.799 7.705 VDR 27.406 26.426 26.847 26.577 8.397 7.850 7.963 8.426 VLDLR 27.166 27.232 28.584 27.543 8.157 8.656 9.700 9.392 XDH Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A ZFP36 24.170 23.980 24.270 24.094 5.161 5.404 5.386 5.943 ZHX3 25.200 24.611 24.418 23.897 6.191 6.035 5.534 5.746 ZNF281 24.066 23.541 23.828 23.343 5.057 4.965 4.944 5.192 ACTB 14.843 14.519 14.721 14.509 −4.166 −4.057 −4.163 −3.642 B2M 19.009 18.576 18.884 18.151 0.000 0.000 0.000 0.000 GAPDH 16.513 16.197 16.551 16.157 −2.496 −2.379 −2.333 −1.994 HPRT1 21.698 21.561 21.777 21.657 2.689 2.985 2.893 3.506 RPLP0 15.187 14.935 15.128 14.595 −3.822 −3.641 −3.756 −3.556 HGDC Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A RTC 21.284 21.345 21.449 21.483 2.275 2.769 2.565 3.332 RTC 21.287 21.410 21.464 21.371 2.278 2.834 2.580 3.220 RTC 21.358 21.384 21.483 21.483 2.349 2.808 2.599 3.332 PPC 18.611 18.672 18.684 18.624 −0.398 0.096 −0.200 0.473 PPC 18.638 19.142 18.699 18.587 −0.371 0.566 −0.185 0.436 PPC 18.646 18.711 19.076 18.685 −0.363 0.135 0.192 0.534 Cpd44 Pred Combo Gene ΔΔCT Fold Change ΔΔCT Fold Change ΔΔCT Fold Change ADARB1 0.046 0.969 1.867 0.274 −0.771 1.706 AFF1 −0.363 1.286 −0.567 1.481 −0.602 1.518 AK2 0.272 0.828 0.053 0.964 0.485 0.714 AMPD3 0.178 0.884 1.259 0.418 1.309 0.404 ANGPTL4 0.119 0.921 0.529 0.693 0.578 0.670 ANXA4 −0.111 1.080 0.305 0.809 0.309 0.807 AQP1 N/A N/A N/A N/A N/A N/A ARID5B 0.334 0.793 0.129 0.914 0.863 0.550 ASPH 0.286 0.820 0.524 0.695 0.884 0.542 ATF4 0.467 0.723 0.282 0.822 0.685 0.622 BCL6 0.227 0.854 0.397 0.759 1.102 0.466 BMPER 1.488 0.357 1.466 0.362 2.477 0.180 CALCR N/A N/A N/A N/A N/A N/A CEBPA −3.545 11.672 −2.341 5.067 −3.150 8.877 CEBPB 0.447 0.734 0.531 0.692 0.948 0.518 COL4A2 2.238 0.212 6.804 0.009 2.687 0.155 CREB1 0.249 0.841 0.085 0.943 0.658 0.634 CREB3 0.344 0.788 0.061 0.959 0.576 0.671 CREB3L4 0.138 0.909 0.336 0.792 0.826 0.564 CTGF −0.518 1.432 0.142 0.906 0.843 0.557 CYB561 −5.412 42.577 1.917 0.265 −2.601 6.067 DDIT4 0.007 0.995 0.296 0.815 −0.128 1.093 DIRAS2 N/A N/A N/A N/A N/A N/A DUSP1 −0.039 1.027 0.387 0.765 0.516 0.699 EDN1 1.460 0.363 1.155 0.449 0.849 0.555 EHD3 −3.030 8.168 −1.092 2.132 −2.783 6.883 ERRFI1 −1.929 3.808 0.235 0.850 −2.079 4.225 FKBP5 −0.032 1.022 −0.948 1.929 −0.615 1.532 FOSL2 −1.462 2.755 −0.099 1.071 −0.984 1.978 GDPD1 0.471 0.721 0.477 0.718 0.722 0.606 GHRHR 2.393 0.190 −1.464 2.759 0.987 0.505 GLUL 0.971 0.510 −1.434 2.702 0.824 0.565 GOT1 0.132 0.913 0.230 0.853 0.311 0.806 H6PD 0.093 0.938 0.377 0.770 0.594 0.663 HAS2 N/A N/A N/A N/A N/A N/A HNRPLL −0.740 1.670 3.085 0.118 1.914 0.265 IL10 N/A N/A N/A N/A N/A N/A IL1RN N/A N/A N/A N/A N/A N/A IL6 N/A N/A N/A N/A N/A N/A IL6R N/A N/A N/A N/A N/A N/A KLF13 −0.098 1.070 −0.280 1.214 −0.328 1.255 KLF9 0.181 0.882 −0.019 1.013 −0.092 1.066 LOX −0.132 1.096 0.721 0.607 0.151 0.901 MERTK −0.108 1.078 0.020 0.986 −0.665 1.586 MT1E N/A N/A N/A N/A N/A N/A MT2A N/A N/A N/A N/A N/A N/A NFKBIA 0.167 0.891 0.064 0.957 0.592 0.663 NR3C1 0.261 0.835 0.317 0.803 0.829 0.563 PDCD7 0.194 0.874 0.021 0.986 0.599 0.660 PDGFRB N/A N/A N/A N/A N/A N/A PDP1 −0.255 1.193 −0.056 1.040 0.325 0.798 PER1 0.206 0.867 0.323 0.799 1.203 0.434 PER2 −0.374 1.296 −0.358 1.282 −0.308 1.238 PIK3R1 −0.032 1.022 −0.202 1.150 0.291 0.817 PLD1 N/A N/A 0.207 0.866 2.143 0.226 PLEKHF1 −0.507 1.421 −0.347 1.272 −0.290 1.223 POU2F1 0.058 0.961 0.395 0.760 0.147 0.903 POU2F2 0.131 0.913 0.145 0.904 0.319 0.802 RASA3 0.917 0.530 0.776 0.584 2.098 0.234 RGS2 0.504 0.705 0.849 0.555 1.707 0.306 RHOB −1.483 2.795 0.626 0.648 −1.101 2.145 RHOJ N/A N/A N/A N/A N/A N/A SESN1 0.055 0.963 −1.262 2.398 −1.375 2.594 SGK1 0.621 0.650 2.120 0.230 2.350 0.196 SLC10A6 2.385 0.191 1.818 0.284 −0.887 1.849 SLC19A2 −0.308 1.238 −0.020 1.014 0.027 0.981 SLC22A5 0.033 0.977 0.648 0.638 0.301 0.812 SNTA1 0.399 0.758 0.665 0.631 1.274 0.414 SPHK1 −1.381 2.604 −0.581 1.496 −1.173 2.255 SPSB1 −0.025 1.017 −0.074 1.053 0.369 0.774 STAT5A −0.033 1.023 −0.227 1.170 0.098 0.934 STAT5B 0.258 0.836 0.254 0.839 0.769 0.587 TBL1XR1 0.030 0.979 0.032 0.978 0.594 0.663 TNF 0.954 0.516 0.753 0.593 0.724 0.605 TNFAIP3 −0.307 1.237 N/A N/A 3.184 0.110 TSC22D3 0.009 0.994 −1.741 3.343 −1.944 3.848 USP2 0.013 0.991 −0.478 1.393 −0.275 1.210 USP54 −0.274 1.209 0.209 0.865 0.115 0.923 VDR −0.547 1.461 −0.434 1.351 0.029 0.980 VLDLR 0.499 0.708 1.543 0.343 1.235 0.425 XDH N/A N/A N/A N/A N/A N/A ZFP36 0.243 0.845 0.225 0.856 0.782 0.582 ZHX3 −0.156 1.114 −0.657 1.577 −0.445 1.361 ZNF281 −0.092 1.066 −0.113 1.081 0.135 0.911 ACTB B2M GAPDH HPRT1 RPLP0 HGDC RTC RTC RTC PPC PPC PPC

TABLE 4c Ct values and fold changes from the RT2 Glucocorticoid signaling PCR array analysis for WSU cell line. Ct Values ΔCT (B2M) Gene DMSO Cpd44 Pred Combo DMSO Cpd44 Pred Combo ADARB1 26.316 25.386 26.108 26.018 6.866 5.701 6.963 5.845 AFF1 28.103 27.925 27.334 26.727 8.653 8.240 8.189 6.554 AK2 20.644 21.365 20.433 22.069 1.194 1.680 1.288 1.896 AMPD3 28.467 27.162 27.943 26.847 9.017 7.477 8.798 6.674 ANGPTL4 31.444 30.487 30.810 31.510 11.994 10.802 11.665 11.337 ANXA4 27.736 24.659 27.406 25.013 8.286 4.974 8.261 4.840 AQP1 Undetermined 33.645 33.595 32.796 N/A 13.960 14.450 12.623 ARID5B 26.244 26.126 26.721 27.140 6.794 6.441 7.576 6.967 ASPH 22.285 22.415 21.939 22.834 2.835 2.730 2.794 2.661 ATF4 19.874 20.470 19.659 20.871 0.424 0.785 0.514 0.698 BCL6 20.954 20.795 20.898 21.133 1.504 1.110 1.753 0.960 BMPER 39.814 Undetermined Undetermined 38.494 20.364 N/A N/A 18.321 CALCR Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CEBPA 28.438 27.014 27.838 27.647 8.988 7.329 8.693 7.474 CEBPB 25.266 26.770 25.775 27.187 5.816 7.085 6.630 7.014 COL4A2 Undetermined Undetermined 34.328 Undetermined N/A N/A 15.183 N/A CREB1 23.170 23.413 22.732 23.778 3.720 3.728 3.587 3.605 CREB3 25.309 25.459 24.551 25.393 5.859 5.774 5.406 5.220 CREB3L4 25.072 24.392 24.437 24.344 5.622 4.707 5.292 4.171 CTGF Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CYB561 36.874 31.478 32.971 33.799 17.424 11.793 13.826 13.626 DDIT4 24.229 24.404 22.252 22.739 4.779 4.719 3.107 2.566 DIRAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A DUSP1 25.679 27.284 25.828 26.552 6.229 7.599 6.683 6.379 EDN1 Undetermined 26.349 30.819 26.407 N/A 6.664 11.674 6.234 EHD3 29.674 24.270 27.724 24.166 10.224 4.585 8.579 3.993 ERRFI1 Undetermined 32.771 Undetermined 32.896 N/A 13.086 N/A 12.723 FKBP5 22.873 23.267 21.321 21.824 3.423 3.582 2.176 1.651 FOSL2 31.109 34.140 33.647 34.690 11.659 14.455 14.502 14.517 GDPD1 28.371 27.494 28.235 27.303 8.921 7.809 9.090 7.130 GHRHR 34.636 39.957 37.789 Undetermined 15.186 20.272 18.644 N/A GLUL Undetermined 28.395 31.475 30.591 N/A 8.710 12.330 10.418 GOT1 22.884 23.827 22.841 24.411 3.434 4.142 3.696 4.238 H6PD 26.360 25.976 26.197 25.435 6.910 6.291 7.052 5.262 HAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A HNRPLL 23.972 24.170 24.750 26.864 4.522 4.485 5.605 6.691 IL10 Undetermined 34.229 34.306 35.010 N/A 14.544 15.161 14.837 IL1RN 32.606 28.388 33.599 29.393 13.156 8.703 14.454 9.220 IL6 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A IL6R Undetermined 33.814 Undetermined Undetermined N/A 14.129 N/A N/A KLF13 24.539 23.800 23.792 23.671 5.089 4.115 4.647 3.498 KLF9 30.841 28.881 30.105 28.187 11.391 9.196 10.960 8.014 LOX 34.266 34.399 34.511 34.207 14.816 14.714 15.366 14.034 MERTK Undetermined 31.323 32.524 Undetermined N/A 11.638 13.379 N/A MT1E Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A MT2A 24.717 23.499 24.518 24.350 5.267 3.814 5.373 4.177 NFKBIA 22.371 23.807 22.895 23.454 2.921 4.122 3.750 3.281 NR3C1 23.250 23.121 23.110 23.300 3.800 3.436 3.965 3.127 PDCD7 24.179 24.740 23.874 25.248 4.729 5.055 4.729 5.075 PDGFRB Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A PDP1 25.371 25.226 24.957 25.536 5.921 5.541 5.812 5.363 PER1 25.109 25.820 24.989 26.651 5.659 6.135 5.844 6.478 PER2 24.451 24.837 24.218 25.563 5.001 5.152 5.073 5.390 PIK3R1 23.734 24.332 23.429 24.080 4.284 4.647 4.284 3.907 PLD1 Undetermined Undetermined 35.266 Undetermined N/A N/A 16.121 N/A PLEKHF1 27.205 28.660 26.977 29.585 7.755 8.975 7.832 9.412 POU2F1 24.234 24.671 24.368 24.732 4.784 4.986 5.223 4.559 POU2F2 23.123 22.678 22.565 22.920 3.673 2.993 3.420 2.747 RASA3 23.952 23.208 23.454 23.293 4.502 3.523 4.309 3.120 RGS2 22.902 24.869 23.962 27.302 3.452 5.184 4.817 7.129 RHOB 29.724 27.234 28.803 27.392 10.274 7.549 9.658 7.219 RHOJ Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A SESN1 28.689 25.215 25.915 21.378 9.239 5.530 6.770 1.205 SGK1 25.579 28.624 27.309 30.174 6.129 8.939 8.164 10.001 SLC10A6 36.617 35.684 37.200 39.653 17.167 15.999 18.055 19.480 SLC19A2 26.638 26.125 25.887 26.101 7.188 6.440 6.742 5.928 SLC22A5 28.901 26.640 29.427 27.488 9.451 6.955 10.282 7.315 SNTA1 24.438 24.181 24.329 25.156 4.988 4.496 5.184 4.993 SPHK1 29.643 29.333 29.804 29.702 10.193 9.648 10.659 9.529 SPSB1 29.613 26.952 29.963 27.294 10.163 7.267 10.818 7.121 STAT5A 25.567 25.495 25.699 24.956 6.117 5.810 6.554 4.783 STAT5B 23.414 23.453 23.270 23.985 3.964 3.768 4.125 3.812 TBL1XR1 21.602 22.111 21.479 22.588 2.152 2.426 2.334 2.415 TNF 23.694 25.079 24.151 25.675 4.244 5.394 5.006 5.502 TNFAIP3 24.946 26.903 26.733 28.675 5.496 7.218 7.588 8.502 TSC22D3 25.514 25.390 22.481 21.679 6.064 5.705 3.336 1.506 USP2 22.646 21.903 20.884 20.640 3.196 2.218 1.739 0.467 USP54 26.549 26.807 26.453 27.306 7.099 7.122 7.308 7.133 VDR 30.102 27.293 29.232 27.319 10.652 7.608 10.087 7.146 VLDLR 28.252 32.346 30.596 Undetermined 8.802 12.661 11.451 N/A XDH Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A ZFP36 24.367 25.541 25.166 26.450 4.917 5.856 6.021 6.277 ZHX3 25.774 24.831 25.570 25.485 6.324 5.146 6.425 5.312 ZNF2B1 24.007 23.913 23.608 24.577 4.557 4.228 4.463 4.404 ACTB 14.801 15.450 14.572 16.143 −4.649 −4.235 −4.573 −4.030 B2M 19.450 19.685 19.145 20.173 0.000 0.000 0.000 0.000 GAPDH 16.528 17.275 16.349 17.416 −2.922 −2.410 −2.796 −2.757 HPRT1 21.509 22.793 21.361 23.732 2.059 3.108 2.216 3.559 RPLP0 15.697 15.681 15.330 15.349 −3.753 −4.004 −3.815 −4.824 HGDC Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A RTC 21.199 20.891 21.392 21.368 1.749 1.206 2.247 1.195 RTC 21.219 20.949 21.293 21.425 1.769 1.264 2.148 1.252 RTC 21.216 20.945 21.237 21.320 1.766 1.260 2.092 1.147 PPC 18.984 18.798 18.835 18.992 −0.466 −0.887 −0.310 −1.181 PPC 18.832 18.877 18.870 18.841 −0.618 −0.808 −0.275 −1.332 PPC 18.869 19.007 18.873 18.835 −0.581 −0.678 −0.272 −1.338 Cpd44 Pred Combo Gene ΔΔCT Fold Change ΔΔCT Fold Change ΔΔCT Fold Change ADARB1 −1.165 2.242 0.097 0.935 −1.021 2.029 AFF1 −0.413 1.331 −0.464 1.379 −2.099 4.284 AK2 0.486 0.714 0.094 0.937 0.702 0.615 AMPD3 −1.540 2.908 −0.219 1.164 −2.343 5.074 ANGPTL4 −1.192 2.285 −0.329 1.256 −0.657 1.577 ANXA4 −3.312 9.931 −0.025 1.017 −3.446 10.898 AQP1 N/A N/A N/A N/A N/A N/A ARID5B −0.353 1.277 0.782 0.582 0.173 0.887 ASPH −0.105 1.075 −0.041 1.029 −0.174 1.128 ATF4 0.361 0.779 0.090 0.940 0.274 0.827 BCL6 −0.394 1.314 0.249 0.841 −0.544 1.458 BMPER N/A N/A N/A N/A −2.043 4.121 CALCR N/A N/A N/A N/A N/A N/A CEBPA −1.659 3.158 −0.295 1.227 −1.514 2.856 CEBPB 1.269 0.415 0.814 0.569 1.198 0.436 COL4A2 N/A N/A N/A N/A N/A N/A CREB1 0.008 0.994 −0.133 1.097 −0.115 1.083 CREB3 −0.085 1.061 −0.453 1.369 −0.639 1.557 CREB3L4 −0.915 1.886 −0.330 1.257 −1.451 2.734 CTGF N/A N/A N/A N/A N/A N/A CYB561 −5.631 49.556 −3.598 12.109 −3.798 13.910 DDIT4 −0.060 1.042 −1.672 3.187 −2.213 4.636 DIRAS2 N/A N/A N/A N/A N/A N/A DUSP1 1.370 0.387 0.454 0.730 0.150 0.901 EDN1 N/A N/A N/A N/A N/A N/A EHD3 −5.639 49.832 −1.645 3.127 −6.231 75.113 ERRFI1 N/A N/A N/A N/A N/A N/A FKBP5 0.159 0.896 −1.247 2.373 −1.772 3.415 FOSL2 2.796 0.144 2.843 0.139 2.858 0.138 GDPD1 −1.112 2.161 0.169 0.889 −1.791 3.461 GHRHR 5.086 0.029 3.458 0.091 N/A N/A GLUL N/A N/A N/A N/A N/A N/A GOT1 0.708 0.612 0.262 0.834 0.804 0.573 H6PD −0.619 1.536 0.142 0.906 −1.648 3.134 HAS2 N/A N/A N/A N/A N/A N/A HNRPLL −0.037 1.026 1.083 0.472 2.169 0.222 IL10 N/A N/A N/A N/A N/A N/A IL1RN −4.453 21.902 1.298 0.407 −3.936 15.306 IL6 N/A N/A N/A N/A N/A N/A IL6R N/A N/A N/A N/A N/A N/A KLF13 −0.974 1.964 −0.442 1.358 −1.591 3.013 KLF9 −2.195 4.579 −0.431 1.348 −3.377 10.389 LOX −0.102 1.073 0.550 0.683 −0.782 1.720 MERTK N/A N/A N/A N/A N/A N/A MT1E N/A N/A N/A N/A N/A N/A MT2A −1.453 2.738 0.106 0.929 −1.090 2.129 NFKBIA 1.201 0.435 0.829 0.563 0.360 0.779 NR3C1 −0.364 1.287 0.165 0.892 −0.673 1.594 PDCD7 0.326 0.798 0.000 1.000 0.346 0.787 PDGFRB N/A N/A N/A N/A N/A N/A PDP1 −0.380 1.301 −0.109 1.078 −0.558 1.472 PER1 0.476 0.719 0.185 0.880 0.819 0.567 PER2 0.151 0.901 0.072 0.951 0.389 0.764 PIK3R1 0.363 0.778 0.000 1.000 −0.377 1.299 PLD1 N/A N/A N/A N/A N/A N/A PLEKHF1 1.220 0.429 0.077 0.948 1.657 0.317 POU2F1 0.202 0.869 0.439 0.738 −0.225 1.169 POU2F2 −0.680 1.602 −0.253 1.192 −0.926 1.900 RASA3 −0.979 1.971 −0.193 1.143 −1.382 2.606 RGS2 1.732 0.301 1.365 0.388 3.677 0.078 RHOB −2.725 6.612 −0.616 1.533 −3.055 8.311 RHOJ N/A N/A N/A N/A N/A N/A SESN1 −3.709 13.077 −2.469 5.537 −8.034 262.105 SGK1 2.810 0.143 2.035 0.244 3.872 0.068 SLC10A6 −1.168 2.247 0.888 0.540 2.313 0.201 SLC19A2 −0.748 1.679 −0.446 1.362 −1.260 2.395 SLC22A5 −2.496 5.641 0.831 0.562 −2.136 4.395 SNTA1 −0.492 1.406 0.196 0.873 0.005 0.997 SPHK1 −0.545 1.459 0.466 0.724 −0.664 1.584 SPSB1 −2.896 7.444 0.655 0.635 −3.042 8.236 STAT5A −0.307 1.237 0.437 0.739 −1.334 2.521 STAT5B −0.196 1.146 0.161 0.894 −0.152 1.111 TBL1XR1 0.274 0.827 0.182 0.881 0.263 0.833 TNF 1.150 0.451 0.762 0.590 1.258 0.418 TNFAIP3 1.722 0.303 2.092 0.235 3.006 0.124 TSC22D3 −0.359 1.283 −2.728 6.625 −4.558 23.556 USP2 −0.978 1.970 −1.457 2.745 −2.729 6.630 USP54 0.023 0.984 0.209 0.865 0.034 0.977 VDR −3.044 8.248 −0.565 1.479 −3.506 11.361 VLDLR 3.859 0.069 2.649 0.159 N/A N/A XDH N/A N/A N/A N/A N/A N/A ZFP36 0.939 0.522 1.104 0.465 1.360 0.390 ZHX3 −1.178 2.263 0.101 0.932 −1.012 2.017 ZNF2B1 −0.329 1.256 −0.094 1.067 −0.153 1.112 ACTB B2M GAPDH HPRT1 RPLP0 HGDC RTC RTC RTC PPC PPC PPC

TABLE 4d Ct values and fold changes from the RT2 Glucocorticoid signaling PCR array analysis for SUDHL10 cell line. H6PD 26.184 28.126 26.256 26.915 7.758 8.979 HAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A HNRPLL 22.972 23.764 22.692 24.016 4.546 4.617 IL10 Undetermined 32.505 Undetermined 32.875 N/A 13.358 IL1RN Undetermined 32.182 Undetermined Undetermined N/A 13.035 IL6 Undetermined Undetermined Undetermined Undetermined N/A N/A IL6R Undetermined 33.807 33.801 Undetermined N/A 14.660 KLF13 25.451 24.536 22.488 22.832 7.025 5.389 KLF9 32.931 32.525 30.255 29.691 14.505 13.378 LOX 33.500 35.385 32.223 32.465 15.074 16.238 MERTK Undetermined 34.652 Undetermined 33.161 N/A 15.505 MT1E Undetermined Undetermined Undetermined 34.503 N/A N/A MT2A 34.844 37.225 35.909 35.849 16.418 18.078 NFKBIA 22.331 23.654 21.628 22.744 3.905 4.507 NR3C1 22.516 23.754 22.000 22.835 4.090 4.617 PDCD7 23.600 25.123 23.256 24.731 5.174 5.976 PDGFRB Undetermined Undetermined Undetermined Undetermined N/A N/A PDP1 25.438 26.175 25.178 26.259 7.012 7.028 PER1 26.209 27.710 24.762 26.686 7.783 8.563 PER2 23.618 24.780 22.642 24.465 5.192 5.633 PIK3R1 23.509 24.661 22.697 23.585 5.083 5.514 PLD1 Undetermined Undetermined Undetermined Undetermined N/A N/A PLEKHF1 27.789 28.979 26.691 27.331 9.363 9.832 POU2F1 25.115 25.842 24.283 24.827 6.689 6.695 POU2F2 23.953 25.098 22.977 24.098 5.527 5.951 RASA3 23.171 24.277 22.449 23.649 4.745 5.130 RGS2 24.794 25.587 25.390 26.161 6.368 6.440 RHOB 28.583 27.829 27.968 26.383 10.157 8.682 RHOJ Undetermined 36.530 Undetermined Undetermined N/A 17.383 SESN1 28.405 27.480 24.220 22.646 9.979 8.333 SGK1 22.694 25.358 22.897 24.642 4.268 6.211 SLC10A6 36.987 37.060 34.670 36.258 18.561 17.913 SLC19A2 31.019 30.597 31.940 31.354 12.593 11.450 SLC22A5 31.275 30.263 32.426 29.324 12.849 11.116 SNTA1 25.751 27.003 24.913 26.374 7.325 7.856 SPHK1 26.852 27.804 25.801 27.082 8.426 8.657 SPSB1 25.856 26.133 24.455 24.642 7.430 6.986 STAT5A 24.170 25.275 23.779 24.550 5.744 6.128 STAT5B 23.533 24.281 23.480 24.231 5.107 5.134 TBL1XR1 20.891 21.846 20.224 21.815 2.465 2.699 TNF 23.208 23.725 22.657 24.669 4.782 4.578 TNFAIP3 26.832 27.677 27.010 26.749 8.406 8.530 TSC22D3 25.441 28.871 23.160 22.809 7.015 9.724 USP2 22.643 23.434 21.579 22.360 4.217 4.287 USP54 27.132 27.789 26.401 27.379 8.706 8.642 VDR 29.507 29.514 28.490 28.525 11.081 10.367 VLDLR 27.937 32.904 31.762 32.093 9.511 13.757 XDH Undetermined Undetermined Undetermined Undetermined N/A N/A ZFP36 25.707 26.643 24.515 25.887 7.281 7.496 ZHX3 26.753 26.305 26.008 26.393 8.327 7.158 ZNF2B1 23.573 23.857 22.336 23.665 5.147 4.710 ACTB 14.330 14.828 13.138 14.548 −4.096 −4.319 B2M 18.426 19.147 17.654 18.834 0.000 0.000 GAPDH 16.544 17.793 15.669 16.935 −1.882 −1.354 HPRT1 19.452 20.615 18.679 20.706 1.026 1.468 RPLP0 15.746 16.821 15.169 15.785 −2.680 −2.326 HGDC Undetermined Undetermined Undetermined Undetermined N/A N/A RTC 22.619 22.346 22.496 23.181 4.193 3.199 RTC 22.626 22.362 22.621 23.201 4.200 3.215 RTC 22.662 22.313 22.484 23.114 4.236 3.166 PPC 18.253 18.442 17.960 18.476 −0.173 −0.705 PPC 18.527 18.474 18.434 18.446 0.101 −0.673 PPC 18.410 18.623 18.515 18.482 −0.016 −0.524 H6PD 8.602 8.081 1.221 0.429 0.844 0.557 0.323 0.799 HAS2 N/A N/A N/A N/A N/A N/A N/A N/A HNRPLL 5.038 5.182 0.071 0.952 0.492 0.711 0.636 0.643 IL10 N/A 14.041 N/A N/A N/A N/A N/A N/A IL1RN N/A N/A N/A N/A N/A N/A N/A N/A IL6 N/A N/A N/A N/A N/A N/A N/A N/A IL6R 16.147 N/A N/A N/A N/A N/A N/A N/A KLF13 4.834 3.998 −1.636 3.108 −2.191 4.566 −3.027 8.151 KLF9 12.601 10.857 −1.127 2.184 −1.904 3.742 −3.648 12.536 LOX 14.569 13.631 1.164 0.446 −0.505 1.419 −1.443 2.719 MERTK N/A 14.327 N/A N/A N/A N/A N/A N/A MT1E N/A 15.669 N/A N/A N/A N/A N/A N/A MT2A 18.255 17.015 1.660 0.316 1.837 0.280 0.597 0.661 NFKBIA 3.974 3.910 0.602 0.659 0.069 0.953 0.005 0.997 NR3C1 4.346 4.001 0.527 0.694 0.256 0.837 −0.089 1.064 PDCD7 5.602 5.897 0.802 0.574 0.428 0.743 0.723 0.606 PDGFRB N/A N/A N/A N/A N/A N/A N/A N/A PDP1 7.524 7.425 0.016 0.989 0.512 0.701 0.413 0.751 PER1 7.108 7.852 0.780 0.582 −0.675 1.597 0.069 0.953 PER2 4.988 5.631 0.441 0.737 −0.204 1.152 0.439 0.738 PIK3R1 5.043 4.751 0.431 0.742 −0.040 1.028 −0.332 1.259 PLD1 N/A N/A N/A N/A N/A N/A N/A N/A PLEKHF1 9.037 8.497 0.469 0.722 −0.326 1.254 −0.866 1.823 POU2F1 6.629 5.993 0.006 0.996 −0.060 1.042 −0.696 1.620 POU2F2 5.323 5.264 0.424 0.745 −0.204 1.152 −0.263 1.200 RASA3 4.795 4.815 0.385 0.766 0.050 0.966 0.070 0.953 RGS2 7.736 7.327 0.072 0.951 1.368 0.387 0.959 0.514 RHOB 10.314 7.549 −1.475 2.780 0.157 0.897 −2.608 6.097 RHOJ N/A N/A N/A N/A N/A N/A N/A N/A SESN1 6.566 3.812 −1.646 3.130 −3.413 10.652 −6.167 71.854 SGK1 5.243 5.808 1.943 0.260 0.975 0.509 1.540 0.344 SLC10A6 17.016 17.424 −0.648 1.567 −1.545 2.918 −1.137 2.199 SLC19A2 14.286 12.520 −1.143 2.208 1.693 0.309 −0.073 1.052 SLC22A5 14.772 10.490 −1.733 3.324 1.923 0.264 −2.359 5.130 SNTA1 7.259 7.540 0.531 0.692 −0.066 1.047 0.215 0.862 SPHK1 8.147 8.248 0.231 0.852 −0.279 1.213 −0.178 1.131 SPSB1 6.801 5.808 −0.444 1.360 −0.629 1.546 −1.622 3.078 STAT5A 6.125 5.716 0.384 0.766 0.381 0.768 −0.028 1.020 STAT5B 5.826 5.397 0.027 0.981 0.719 0.608 0.290 0.818 TBL1XR1 2.570 2.981 0.234 0.850 0.105 0.930 0.516 0.699 TNF 5.003 5.835 −0.204 1.152 0.221 0.858 1.053 0.482 TNFAIP3 9.356 7.915 0.124 0.918 0.950 0.518 −0.491 1.405 TSC22D3 5.506 3.975 2.709 0.153 −1.509 2.846 −3.040 8.225 USP2 3.925 3.526 0.070 0.953 −0.292 1.224 −0.691 1.614 USP54 8.747 8.545 −0.064 1.045 0.041 0.972 −0.161 1.118 VDR 10.836 9.691 −0.714 1.640 −0.245 1.185 −1.390 2.621 VLDLR 14.108 13.259 4.246 0.053 4.597 0.041 3.748 0.074 XDH N/A N/A N/A N/A N/A N/A N/A N/A ZFP36 6.861 7.053 0.215 0.862 −0.420 1.338 −0.228 1.171 ZHX3 8.354 7.559 −1.169 2.249 0.027 0.981 −0.768 1.703 ZNF2B1 4.682 4.831 −0.437 1.354 −0.465 1.380 −0.316 1.245 ACTB −4.516 −4.286 B2M 0.000 0.000 GAPDH −1.985 −1.899 HPRT1 1.025 1.872 RPLP0 −2.485 −3.049 HGDC N/A N/A RTC 4.842 4.347 RTC 4.967 4.367 RTC 4.830 4.280 PPC 0.306 −0.358 PPC 0.780 −0.388 PPC 0.861 −0.352

TABLE 4e Ct values and fold changes from the RT2 Glucocorticoid signaling PCR array analysis for RI cell line. Ct Values ΔCT (B2M) Gene DMSO Cpd44 Pred Combo DMSO Cpd44 Pred Combo ADARB1 27.745 26.650 28.557 28.623 8.964 7.292 9.377 9.377 AFF1 28.249 26.820 27.258 26.977 9.468 7.462 8.078 7.731 AK2 19.425 20.270 20.510 21.466 0.644 0.912 1.330 2.220 AMPD3 27.499 27.191 27.354 27.238 8.718 7.833 8.174 7.992 ANGPTL4 30.178 29.820 32.245 29.596 11.397 10.462 13.065 10.350 ANXA4 24.380 24.395 24.910 24.771 5.599 5.037 5.730 5.525 AQP1 Undetermined Undetermined Undetermined 33.328 N/A N/A N/A 14.082 ARID5B 27.976 27.333 29.208 28.495 9.195 7.975 10.028 9.249 ASPH 22.413 23.466 23.583 24.410 3.632 4.108 4.403 5.164 ATF4 17.689 18.269 19.452 20.540 −1.092 −1.089 0.272 1.294 BCL6 19.449 20.289 20.785 20.772 0.668 0.931 1.605 1.526 BMPER Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CALCR Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CEBPA Undetermined 36.511 Undetermined Undetermined N/A 17.153 N/A N/A CEBPB 23.192 23.765 26.229 27.211 4.411 4.407 7.049 7.965 COL4A2 31.978 31.782 Undetermined 35.212 13.197 12.424 N/A 15.966 CREB1 22.435 23.217 23.317 23.470 3.654 3.859 4.137 4.224 CREB3 23.790 24.178 24.951 24.735 5.009 4.820 5.771 5.489 CREB3L4 23.683 23.500 24.211 23.870 4.902 4.142 5.031 4.624 CTGF Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CYB561 39.352 38.452 38.088 37.618 20.571 19.094 18.908 18.372 DDIT4 21.641 22.679 23.471 22.583 2.860 3.321 4.291 3.337 DIRAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A DUSP1 25.166 25.422 25.412 24.981 6.385 6.064 6.232 5.735 EDN1 32.446 31.815 39.440 30.700 13.665 12.457 20.260 11.454 EHD3 24.957 24.572 25.411 23.975 6.176 5.214 6.231 4.729 ERRFI1 Undetermined 31.705 32.655 31.791 N/A 12.347 13.475 12.545 FKBP5 20.792 21.757 20.858 20.881 2.011 2.399 1.678 1.635 FOSL2 31.458 30.761 34.157 36.459 12.677 11.403 14.977 17.213 GDPD1 27.589 27.394 28.699 28.110 8.808 8.036 9.519 8.864 GHRHR Undetermined 37.546 33.555 29.797 N/A 18.188 14.375 10.551 GLUL 30.775 28.738 32.181 32.961 11.994 9.380 13.001 13.715 GOT1 21.489 22.584 23.355 24.551 2.708 3.226 4.175 5.305 H6PD 25.108 25.012 26.442 24.742 6.327 5.654 7.262 5.496 HAS2 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A HNRPLL 21.958 22.844 23.146 24.289 3.177 3.486 3.966 5.043 IL10 32.353 31.498 32.669 Undetermined 13.572 12.140 13.489 N/A IL1RN 29.709 28.405 29.300 29.204 10.928 9.047 10.120 9.958 IL6 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A IL6R 29.184 29.246 30.468 31.321 10.403 9.888 11.288 12.075 KLF13 22.843 22.854 23.590 23.322 4.062 3.496 4.410 4.076 KLF9 34.469 Undetermined Undetermined Undetermined 15.688 N/A N/A N/A LOK 33.918 33.915 34.185 33.948 15.137 14.557 15.005 14.702 MERTK 34.533 30.691 Undetermined 31.272 15.752 11.333 N/A 12.026 MT1E Undetermined 34.215 Undetermined Undetermined N/A 14.857 N/A N/A MT2A 23.125 24.279 25.180 25.570 4.344 4.921 6.000 6.324 NFKBIA 22.279 23.710 23.531 23.442 3.498 4.352 4.351 4.196 NR3C1 21.972 22.616 23.323 23.237 3.191 3.258 4.143 3.991 PDCD7 23.823 24.406 24.616 24.925 5.042 5.048 5.436 5.679 PDGFRB Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A PDP1 25.799 25.387 26.940 25.667 7.018 6.029 7.760 6.421 PER1 24.531 25.492 27.160 26.707 5.750 6.134 7.980 7.461 PER2 24.162 24.378 24.811 24.547 5.381 5.020 5.631 5.301 PIK3R1 22.958 23.908 24.331 24.602 4.177 4.550 5.151 5.356 PLD1 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A PLEKHF1 29.893 30.520 31.367 34.212 11.112 11.162 12.187 14.966 POU2F1 23.693 24.243 25.222 25.607 4.912 4.885 6.042 6.361 POU2F2 21.776 21.769 22.972 22.359 2.995 2.411 3.792 3.113 RASA3 25.711 26.279 27.653 26.571 6.930 6.921 8.473 7.325 RGS2 25.306 25.721 26.477 28.212 6.525 6.363 7.297 8.966 RHOB Undetermined Undetermined Undetermined 38.682 N/A N/A N/A 19.436 RHOJ Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A SESN1 25.545 24.425 21.882 20.973 6.764 5.067 2.702 1.727 SGK1 24.884 26.262 26.131 26.411 6.103 6.904 6.951 7.165 SLC10A6 35.730 Undetermined 34.404 35.950 16.949 N/A 15.224 16.704 SLC19A2 25.756 25.536 26.202 25.342 6.975 6.178 7.022 6.096 SLC22A5 32.280 Undetermined Undetermined 38.888 13.499 N/A N/A 19.642 SNTA1 24.937 25.554 26.480 26.133 6.156 6.196 7.300 6.887 SPHK1 31.323 31.119 34.340 Undetermined 12.542 11.761 15.160 N/A SPSB1 26.573 26.285 28.977 28.200 7.792 6.927 9.797 8.954 STAT5A 22.191 22.769 23.379 22.666 3.410 3.411 4.199 3.420 STAT5B 22.200 22.683 23.111 23.737 3.419 3.325 3.931 4.491 TBL1XR1 20.394 21.663 21.587 21.692 1.613 2.305 2.407 2.446 TNF 24.972 24.712 24.773 22.812 6.191 5.354 5.593 3.566 TNFAIP3 25.433 26.896 27.393 28.474 6.652 7.538 8.213 9.228 TSC22D3 22.534 23.300 21.502 21.179 3.753 3.942 2.322 1.933 USP2 20.982 21.420 20.720 20.616 2.201 2.062 1.540 1.370 USP54 26.748 26.364 27.638 26.992 7.967 7.006 8.458 7.746 VDR 29.817 27.736 31.463 29.508 11.036 8.378 12.283 10.262 VLDLR 35.442 Undetermined 33.979 Undetermined 16.661 N/A 14.799 N/A XDH Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A ZFP36 23.833 24.374 25.160 24.997 5.052 5.016 5.980 5.751 ZHX3 24.547 29.785 25.114 24.601 5.766 10.427 5.934 5.355 ZNF281 23.044 23.667 23.814 23.669 4.263 4.309 4.634 4.423 ACTB 14.794 15.664 15.466 15.976 −3.987 −3.694 −3.714 −3.270 B2M 18.781 19.358 19.180 19.246 0.000 0.000 0.000 0.000 GAPDH 15.388 15.720 16.234 17.444 −3.393 −3.638 −2.946 −1.802 HPRT1 21.297 22.013 21.626 22.777 2.516 2.655 2.446 3.531 RPLP0 15.092 14.837 15.994 15.962 −3.689 −4.521 −3.186 −3.284 HGDC Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A RTC 20.832 21.659 20.818 20.383 2.051 2.301 1.638 1.137 RTC 20.752 21.713 20.681 20.380 1.971 2.355 1.501 1.134 RTC 20.792 21.629 20.780 20.481 2.011 2.271 1.600 1.235 PPC 18.493 18.197 18.424 18.380 −0.288 −1.161 −0.756 −0.866 PPC 18.567 18.303 18.491 18.255 −0.214 −1.055 −0.689 −0.991 PPC 18.444 18.435 18.381 18.325 −0.337 −0.923 −0.799 −0.921 Cpd44 Pred Combo Gene ΔΔCT Fold Change ΔΔCT Fold Change ΔΔCT Fold Change ADARB1 −1.672 3.187 0.413 0.751 0.413 0.751 AFF1 −2.006 4.017 −1.390 2.621 −1.737 3.333 AK2 0.268 0.830 0.686 0.622 1.576 0.335 AMPD3 −0.885 1.847 −0.544 1.458 −0.726 1.654 ANGPTL4 −0.935 1.912 1.668 0.315 −1.047 2.066 ANXA4 −0.562 1.476 0.131 0.913 −0.074 1.053 AQP1 N/A N/A N/A N/A N/A N/A ARID5B −1.220 2.329 0.833 0.561 0.054 0.963 ASPH 0.476 0.719 0.771 0.586 1.532 0.346 ATF4 0.003 0.998 1.364 0.389 2.386 0.191 BCL6 0.263 0.833 0.937 0.522 0.858 0.552 BMPER N/A N/A N/A N/A N/A N/A CALCR N/A N/A N/A N/A N/A N/A CEBPA N/A N/A N/A N/A N/A N/A CEBPB −0.004 1.003 2.638 0.161 3.554 0.085 COL4A2 −0.773 1.709 N/A N/A 2.769 0.147 CREB1 0.205 0.868 0.483 0.715 0.570 0.674 CREB3 −0.189 1.140 0.762 0.590 0.480 0.717 CREB3L4 −0.760 1.693 0.129 0.914 −0.278 1.213 CTGF N/A N/A N/A N/A N/A N/A CYB561 −1.477 2.784 −1.663 3.167 −2.199 4.592 DDIT4 0.461 0.726 1.431 0.371 0.477 0.718 DIRAS2 N/A N/A N/A N/A N/A N/A DUSP1 −0.321 1.249 −0.153 1.112 −0.650 1.569 EDN1 −1.208 2.310 6.595 0.010 −2.211 4.630 EHD3 −0.962 1.948 0.055 0.963 −1.447 2.726 ERRFI1 N/A N/A N/A N/A N/A N/A FKBP5 0.388 0.764 −0.333 1.260 −0.376 1.298 FOSL2 −1.274 2.418 2.300 0.203 4.536 0.043 GDPD1 −0.772 1.708 0.711 0.611 0.056 0.962 GHRHR N/A N/A N/A N/A N/A N/A GLUL −2.614 6.122 1.007 0.498 1.721 0.303 GOT1 0.518 0.698 1.467 0.362 2.597 0.165 H6PD −0.673 1.594 0.935 0.523 −0.831 1.779 HAS2 N/A N/A N/A N/A N/A N/A HNRPLL 0.309 0.807 0.789 0.579 1.866 0.274 IL10 −1.432 2.698 −0.083 1.059 N/A N/A IL1RN −1.881 3.683 −0.808 1.751 −0.970 1.959 IL6 N/A N/A N/A N/A N/A N/A IL6R −0.515 1.429 0.885 0.541 1.672 0.314 KLF13 −0.566 1.480 0.348 0.786 0.014 0.990 KLF9 N/A N/A N/A N/A N/A N/A LOK −0.580 1.495 −0.132 1.096 −0.435 1.352 MERTK −4.419 21.392 N/A N/A −3.726 13.232 MT1E N/A N/A N/A N/A N/A N/A MT2A 0.577 0.670 1.656 0.317 1.980 0.253 NFKBIA 0.854 0.553 0.853 0.554 0.698 0.616 NR3C1 0.067 0.955 0.952 0.517 0.800 0.574 PDCD7 0.006 0.996 0.394 0.761 0.637 0.643 PDGFRB N/A N/A N/A N/A N/A N/A PDP1 −0.989 1.985 0.742 0.598 −0.597 1.513 PER1 0.384 0.766 2.230 0.213 1.711 0.305 PER2 −0.361 1.284 0.250 0.841 −0.080 1.057 PIK3R1 0.373 0.772 0.974 0.509 1.179 0.442 PLD1 N/A N/A N/A N/A N/A N/A PLEKHF1 0.050 0.966 1.075 0.475 3.854 0.069 POU2F1 −0.027 1.019 1.130 0.457 1.449 0.366 POU2F2 −0.584 1.499 0.797 0.576 0.118 0.921 RASA3 −0.009 1.006 1.543 0.343 0.395 0.760 RGS2 −0.162 1.119 0.772 0.586 2.441 0.184 RHOB N/A N/A N/A N/A N/A N/A RHOJ N/A N/A N/A N/A N/A N/A SESN1 −1.697 3.242 −4.062 16.703 −5.037 32.831 SGK1 0.801 0.574 0.848 0.556 1.062 0.479 SLC10A6 N/A N/A −1.725 3.306 −0.245 1.185 SLC19A2 −0.797 1.737 0.047 0.968 −0.879 1.839 SLC22A5 N/A N/A N/A N/A 6.143 0.014 SNTA1 0.040 0.973 1.144 0.453 0.731 0.602 SPHK1 −0.781 1.718 2.618 0.163 N/A N/A SPSB1 −0.865 1.821 2.005 0.249 1.162 0.447 STAT5A 0.001 0.999 0.789 0.579 0.010 0.993 STAT5B −0.094 1.067 0.512 0.701 1.072 0.476 TBL1XR1 0.692 0.619 0.794 0.577 0.833 0.561 TNF −0.837 1.786 −0.598 1.514 −2.625 6.169 TNFAIP3 0.886 0.541 1.561 0.339 2.576 0.168 TSC22D3 0.189 0.877 −1.431 2.696 −1.820 3.531 USP2 −0.139 1.101 −0.661 1.581 −0.831 1.779 USP54 −0.961 1.947 0.491 0.712 −0.221 1.166 VDR −2.658 6.312 1.247 0.421 −0.774 1.710 VLDLR N/A N/A −1.862 3.635 N/A N/A XDH N/A N/A N/A N/A N/A N/A ZFP36 −0.036 1.025 0.928 0.526 0.699 0.616 ZHX3 4.661 0.040 0.168 0.890 −0.411 1.330 ZNF281 0.046 0.969 0.371 0.773 0.160 0.895 ACTB B2M GAPDH HPRT1 RPLP0 HGDC RTC RTC RTC PPC PPC PPC

TABLE 4f Ct values and fold changes from the RT2 Glucocorticoid signaling PCR array analysis for SUDHL4 cell line. Ct Values ΔCT (B2M) Gene DMSO Cpd44 Pred Combo DMSO Cpd44 Pred Combo ADARB1 27.696 28.562 27.634 28.373 10.107 8.878 9.591 8.992 AFF1 26.492 25.936 25.874 25.660 7.394 7.118 6.965 7.788 AK2 19.861 20.311 20.602 20.682 2.416 1.846 1.340 1.157 AMPD3 25.234 25.553 24.780 25.739 7.473 6.024 6.582 6.530 ANGPTL4 29.764 29.825 29.326 30.167 11.901 10.570 10.854 11.060 ANXA4 26.847 28.717 26.973 28.902 10.636 8.217 9.746 8.143 AQP1 Undetermined Undetermined 32.982 32.161 13.895 14.226 N/A N/A ARID5B 25.120 25.129 24.504 24.555 6.289 5.748 6.158 6.416 ASPH 22.618 23.348 22.741 23.094 4.828 3.985 4.377 3.914 ATF4 19.323 18.778 18.988 18.352 0.086 0.232 −0.193 0.619 BCL6 20.521 21.075 20.634 21.163 2.897 1.878 2.104 1.817 BMPER Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CALCR Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CEBPA 28.837 31.206 28.782 30.802 12.536 10.026 12.235 10.133 CEBPB 24.507 23.911 23.944 22.678 4.412 5.188 4.940 5.803 COL4A2 Undetermined Undetermined Undetermined 33.904 15.638 N/A N/A N/A CREB1 22.906 22.973 22.993 22.816 4.550 4.237 4.002 4.202 CREB3 24.330 24.566 24.421 24.421 6.155 5.665 5.595 5.626 CREB3L4 24.709 25.089 24.418 24.583 6.317 5.662 6.118 6.005 CTGF Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A CYB561 33.993 36.737 33.006 36.752 18.486 14.250 17.766 15.289 DDIT4 21.247 21.455 21.854 22.681 4.415 3.098 2.484 2.543 DIRAS2 Undetermined Undetermined 33.382 Undetermined N/A 14.626 N/A N/A DUSP1 26.436 26.325 26.754 26.713 8.447 7.998 7.354 7.732 EDN1 32.440 33.297 32.372 Undetermined N/A 13.616 14.326 13.736 EHD3 24.298 25.766 24.878 26.386 8.120 6.122 6.795 5.594 ERRFI1 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A FKBP5 20.533 20.494 21.869 21.371 3.105 3.113 1.523 1.829 FOSL2 35.083 31.757 33.362 Undetermined N/A 14.606 12.786 16.379 GDPD1 27.358 28.134 26.972 27.838 9.572 8.216 9.163 8.654 GHRHR 36.313 37.623 Undetermined 36.734 18.468 N/A 18.652 17.609 GLUL 35.436 35.795 34.414 Undetermined N/A 15.658 16.824 16.732 GOT1 22.400 22.607 22.859 22.304 4.038 4.103 3.636 3.696 H6PD 25.209 25.743 24.819 24.878 6.612 6.063 6.772 6.505 HAS2 Undetermined 35.628 31.961 Undetermined N/A 13.205 16.657 N/A HNRPLL 22.667 22.977 22.577 22.558 4.292 3.821 4.006 3.963 IL10 32.210 33.099 31.119 32.524 14.258 12.363 14.128 13.506 IL1RN Undetermined Undetermined 36.259 Undetermined N/A 17.503 N/A N/A IL6 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A IL6R 32.607 33.589 31.995 33.408 15.142 13.239 14.618 13.903 KLF13 22.256 22.649 22.834 22.878 4.612 4.078 3.678 3.552 KLF9 26.816 27.456 26.769 27.572 9.306 8.013 8.485 8.112 LOX 33.947 Undetermined Undetermined Undetermined N/A N/A N/A 15.243 MERTK 33.257 Undetermined 33.859 31.392 13.126 15.103 N/A 14.553 MT1E Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A MT2A 23.416 24.175 23.522 23.341 5.075 4.766 5.204 4.712 NFKBIA 22.744 22.909 23.016 22.914 4.648 4.260 3.938 4.040 NR3C1 22.602 22.803 22.781 22.525 4.259 4.025 3.832 3.898 PDCD7 23.859 24.858 24.113 23.750 5.484 5.357 5.887 5.155 PDGFRB Undetermined Undetermined 35.205 Undetermined N/A 16.449 N/A N/A PDP1 25.255 26.112 25.507 25.928 7.662 6.751 7.141 6.551 PER1 24.612 24.926 24.973 25.007 6.741 6.217 5.955 5.908 PER2 23.794 24.371 24.403 24.767 6.501 5.647 5.400 5.090 PIK3R1 23.210 23.440 23.615 23.627 5.361 4.859 4.469 4.506 PLD1 Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A PLEKHF1 27.292 27.868 27.684 28.448 10.182 8.928 8.897 8.588 POU2F1 23.799 24.224 23.866 23.951 5.685 5.110 5.253 5.095 POU2F2 21.502 21.920 21.841 21.890 3.624 3.085 2.949 2.798 RASA3 22.754 23.207 22.984 23.225 4.959 4.228 4.236 4.050 RGS2 24.883 25.145 24.670 24.812 6.546 5.914 6.174 6.179 RHOB 30.760 32.584 30.084 31.155 12.889 11.328 13.613 12.056 RHOJ Undetermined Undetermined 38.493 Undetermined N/A 19.737 N/A N/A SESN1 22.189 Undetermined 25.195 26.963 8.697 6.439 N/A 3.485 SGK1 25.886 25.808 26.513 25.449 7.183 7.757 6.837 7.182 SLC10A6 37.655 34.857 34.336 38.026 19.760 15.580 15.886 18.951 SLC19A2 26.295 27.465 26.633 27.755 9.489 7.877 8.494 7.591 SLC22A5 27.847 28.544 27.725 28.010 9.744 8.969 9.573 9.143 SNTA1 24.008 24.797 24.422 24.779 6.513 5.666 5.826 5.304 SPHK1 29.372 30.619 29.007 29.583 11.317 10.251 11.648 10.668 SPSB1 25.736 26.495 25.588 25.722 7.456 6.832 7.524 7.032 STAT5A 24.652 25.174 24.761 24.858 6.592 6.005 6.203 5.948 STAT5B 21.986 22.153 21.908 21.716 3.450 3.152 3.182 3.282 TBL1XR1 20.756 20.805 20.855 20.821 2.555 2.099 1.834 2.052 TNF 27.723 29.337 29.509 31.477 13.211 10.753 10.366 9.019 TNFAIP3 28.965 28.521 27.807 26.978 8.712 9.051 9.550 10.261 TSC22D3 21.819 21.432 23.384 22.896 4.630 4.628 2.461 3.115 USP2 20.842 21.342 22.120 22.318 4.052 3.364 2.371 2.138 USP54 26.333 26.952 33.990 27.307 9.041 15.234 7.981 7.629 VDR 27.497 28.330 26.956 28.621 10.355 8.200 9.359 8.793 VLDLR 30.410 28.792 27.824 26.896 8.630 9.068 9.821 11.706 XDH Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A ZFP36 24.716 24.706 24.770 24.542 6.276 6.014 5.735 6.012 ZHX3 24.009 24.719 24.325 24.882 6.616 5.569 5.748 5.305 ZNF281 23.423 23.881 23.813 23.935 5.669 5.057 4.910 4.719 ACTB 13.717 14.247 14.284 14.272 −3.994 −4.472 −4.724 −4.987 B2M 18.704 18.971 18.756 18.266 0.000 0.000 0.000 0.000 GAPDH 15.435 15.835 15.790 15.782 −2.484 −2.966 −3.136 −3.269 HPRT1 21.349 21.358 21.582 21.214 2.948 2.826 2.387 2.645 RPLP0 15.192 15.469 15.266 15.194 −3.072 −3.490 −3.502 −3.512 HGDC Undetermined Undetermined Undetermined Undetermined N/A N/A N/A N/A RTC 21.372 21.163 21.388 21.673 3.407 2.632 2.192 2.668 RTC 21.441 21.008 21.369 21.554 3.288 2.613 2.037 2.737 RTC 21.504 21.137 21.357 21.500 3.234 2.601 2.166 2.800 PPC 18.529 18.295 18.338 18.368 0.102 −0.418 −0.676 −0.175 PPC 18.544 18.326 19.432 18.405 0.139 0.676 −0.645 −0.160 PPC 18.784 18.935 18.081 18.679 0.413 −0.675 −0.036 0.080 Cpd44 Pred Combo Gene ΔΔCT Fold Change ΔΔCT Fold Change ΔΔCT Fold Change ADARB1 −1.229 2.344 −0.516 1.430 −1.115 2.166 AFF1 −0.276 1.211 −0.429 1.346 0.394 0.761 AK2 −0.570 1.485 −1.076 2.108 −1.259 2.393 AMPD3 −1.449 2.730 −0.891 1.854 −0.943 1.923 ANGPTL4 −1.331 2.516 −1.047 2.066 −0.841 1.791 ANXA4 −2.419 5.348 −0.890 1.853 −2.493 5.629 AQP1 0.331 0.795 N/A N/A N/A N/A ARID5B −0.541 1.455 −0.131 1.095 0.127 0.916 ASPH −0.843 1.794 −0.451 1.367 −0.914 1.884 ATF4 0.146 0.904 −0.279 1.213 0.533 0.691 BCL6 −1.019 2.027 −0.793 1.733 −1.080 2.114 BMPER N/A N/A N/A N/A N/A N/A CALCR N/A N/A N/A N/A N/A N/A CEBPA −2.510 5.696 −0.301 1.232 −2.403 5.289 CEBPB 0.776 0.584 0.528 0.694 1.391 0.381 COL4A2 N/A N/A N/A N/A N/A N/A CREB1 −0.313 1.242 −0.548 1.462 −0.348 1.273 CREB3 −0.490 1.404 −0.560 1.474 −0.529 1.443 CREB3L4 −0.655 1.575 −0.199 1.148 −0.312 1.241 CTGF N/A N/A N/A N/A N/A N/A CYB561 −4.236 18.844 −0.720 1.647 −3.197 9.170 DDIT4 −1.317 2.491 −1.931 3.813 −1.872 3.660 DIRAS2 N/A N/A N/A N/A N/A N/A DUSP1 −0.449 1.365 −1.093 2.133 −0.715 1.641 EDN1 N/A N/A N/A N/A N/A N/A EHD3 −1.998 3.994 −1.325 2.505 −2.526 5.760 ERRFI1 N/A N/A N/A N/A N/A N/A FKBP5 0.008 0.994 −1.582 2.994 −1.276 2.422 FOSL2 N/A N/A N/A N/A N/A N/A GDPD1 −1.356 2.560 −0.409 1.328 −0.918 1.889 GHRHR N/A N/A 0.184 0.880 −0.859 1.814 GLUL N/A N/A N/A N/A N/A N/A GOT1 0.065 0.956 −0.402 1.321 −0.342 1.268 H6PD −0.549 1.463 0.160 0.895 −0.107 1.077 HAS2 N/A N/A N/A N/A N/A N/A HNRPLL −0.471 1.386 −0.286 1.219 −0.329 1.256 IL10 −1.895 3.719 −0.130 1.094 −0.752 1.684 IL1RN N/A N/A N/A N/A N/A N/A IL6 N/A N/A N/A N/A N/A N/A IL6R −1.903 3.740 −0.524 1.438 −1.239 2.360 KLF13 −0.534 1.448 −0.934 1.911 −1.060 2.085 KLF9 −1.293 2.450 −0.821 1.767 −1.194 2.288 LOX N/A N/A N/A N/A N/A N/A MERTK 1.977 0.254 N/A N/A 1.427 0.372 MT1E N/A N/A N/A N/A N/A N/A MT2A −0.309 1.239 0.129 0.914 −0.363 1.286 NFKBIA −0.388 1.309 −0.710 1.636 −0.608 1.524 NR3C1 −0.234 1.176 −0.427 1.344 −0.361 1.284 PDCD7 −0.127 1.092 0.403 0.756 −0.329 1.256 PDGFRB N/A N/A N/A N/A N/A N/A PDP1 −0.911 1.880 −0.521 1.435 −1.111 2.160 PER1 −0.524 1.438 −0.786 1.724 −0.833 1.781 PER2 −0.854 1.808 −1.101 2.145 −1.411 2.659 PIK3R1 −0.502 1.416 −0.892 1.856 −0.855 1.809 PLD1 N/A N/A N/A N/A N/A N/A PLEKHF1 −1.254 2.385 −1.285 2.437 −1.594 3.019 POU2F1 −0.575 1.490 −0.432 1.349 −0.590 1.505 POU2F2 −0.539 1.453 −0.675 1.597 −0.826 1.773 RASA3 −0.731 1.660 −0.723 1.651 −0.909 1.878 RGS2 −0.632 1.550 −0.372 1.294 −0.367 1.290 RHOB −1.561 2.951 0.724 0.605 −0.833 1.781 RHOJ N/A N/A N/A N/A N/A N/A SESN1 −2.258 4.783 N/A N/A −5.212 37.065 SGK1 0.574 0.672 −0.346 1.271 −0.001 1.001 SLC10A6 −4.180 18.126 −3.874 14.662 −0.809 1.752 SLC19A2 −1.612 3.057 −0.995 1.993 −1.898 3.727 SLC22A5 −0.775 1.711 −0.171 1.126 −0.601 1.517 SNTA1 −0.847 1.799 −0.687 1.610 −1.209 2.312 SPHK1 −1.066 2.094 0.331 0.795 −0.649 1.568 SPSB1 −0.624 1.541 0.068 0.954 −0.424 1.342 STAT5A −0.587 1.502 −0.389 1.309 −0.644 1.563 STAT5B −0.298 1.229 −0.268 1.204 −0.168 1.123 TBL1XR1 −0.456 1.372 −0.721 1.648 −0.503 1.417 TNF −2.458 5.495 −2.845 7.185 −4.192 18.278 TNFAIP3 0.339 0.791 0.838 0.559 1.549 0.342 TSC22D3 −0.002 1.001 −2.169 4.497 −1.515 2.858 USP2 −0.688 1.611 −1.681 3.207 −1.914 3.769 USP54 6.193 0.014 −1.060 2.085 −1.412 2.661 VDR −2.155 4.454 −0.996 1.994 −1.562 2.953 VLDLR 0.438 0.738 1.191 0.438 3.076 0.119 XDH N/A N/A N/A N/A N/A N/A ZFP36 −0.262 1.199 −0.541 1.455 −0.264 1.201 ZHX3 −1.047 2.066 −0.868 1.825 −1.311 2.481 ZNF281 −0.612 1.528 −0.759 1.692 −0.950 1.932 ACTB B2M GAPDH HPRT1 RPLP0 HGDC RTC RTC RTC PPC PPC PPC

Example 3: Inhibition of EZH2 Overcomes Resistance to Sunitinib in Clear Cell Renal Cell Carcinoma Models

Alterations in epigenetic mechanisms including histone modification and hypermethylation at gene promoter regions have been implicated as mechanisms of drug resistance in cancer. Alternation of epigenetic regulators such histone methyltransferase, EZH2, has been reported in numerous cancer types including advanced renal cell carcinoma (RCC). Previous studies suggest that sunitinib may have a direct anti-tumor effect and that acquired sunitinib resistance may be induced in tumor cells rather than just in endothelial cells. In this study, the role of EZH2 was investigated in sunitinib resistance in clear cell renal cell carcinoma.

Methods:

Human RCC cell lines 786-0 were treated and exposed to increasing concentrations of sunitinib to develop a resistant cell line, 786-0R. Parental and resistant cell lines were treated with either sunitinib, GSK126 (EZH2 inhibitor) or both. In parallel, EZH2 was knocked down in 786-0 cells and exposed to increasing concentrations of sunitinib. Cell viability was quantitated by absorbance of crystal violet stained cells using a spectrometer at 570 nm. In a second set of experiments, control and treated cells were collected for western analysis. Mice bearing human ccRCC patient derived xenograft (PDXs); RP-R-01, RP-R-02 and RP-R-02LM (a metastatic ccRCC model established from RP-R-02) were implanted into SCID mice. When tumors reached an average volume of 50 mm³, mice were randomly grouped into 2 arms; control, sunitinib treatment (40 mg/kg, 5 days/week) or EZH2i EPZ011989 (500 mg/kg, 2×/day, 5 days/week). Tumors volumes and body weight were assessed once per week. Tumor tissues and lungs were collected for immunohistochemistry analysis. All assessments and quantification were done blindly.

Results:

The in vitro and in vivo data showed an increased expression of EZH2 with resistance to sunitinib. Furthermore, inhibition of EZH2 in the in vitro and in vivo studies correlated with a significant increase in the anti-tumor effect of sunitinib in both parental and resistant cell lines.

CONCLUSION

Overall, the data suggest the potential role of epigenetic alterations, specifically EZH2 overexpression and its association with resistance to sunitinib.

All publications and patent documents cited herein are incorporated herein by reference as if each such publication or document was specifically and individually indicated to be incorporated herein by reference. Citation of publications and patent documents is not intended as an admission that any is pertinent prior art, nor does it constitute any admission as to the contents or date of the same. The invention having now been described by way of written description, those of skill in the art will recognize that the invention can be practiced in a variety of embodiments and that the foregoing description and examples below are for purposes of illustration and not limitation of the claims that follow.

The invention can be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein. 

1. A method for treating cancer in a patient in need thereof comprising administering a therapeutically effective amount of an EZH2 inhibitor and one or more tyrosine kinase inhibitors.
 2. The method of claim 1, wherein the cancer is resistant to tyrosine kinase inhibitor treatment.
 3. The method of claim 1, wherein the one or more tyrosine kinase inhibitors are VEGF/VEGFR inhibitors.
 4. A method for treating cancer in a patient in need thereof comprising administering a therapeutically effective amount of an EZH2 inhibitor and one or more VEGF/VEGFR inhibitors.
 5. The method of claim 1, wherein the cancer is resistant to VEGF/VEGFR inhibitor treatment.
 6. The method of claim 1, wherein the EZH2 inhibitor is Compound 44 having the following formula:

(Compound 44) or pharmaceutically acceptable salt thereof.
 7. The method of claim 1, wherein the EZH2 inhibitor is:

or pharmaceutically acceptable salt thereof.
 8. The method of claim 1, wherein the EZH2 inhibitor is GSK-126.
 9. The method of claim 1, wherein the one or more tyrosine kinase inhibitors are selected from erlotinib (Tarceva); gefitinib (Iressa); imatinib (Gleevec); sorafenib (Nexavar); sunitinib (Sutent); trastuzumab (Herceptin); bevacizumab (Avastin); rituximab (Rituxan); lapatinib (Tykerb); cetuximab (Erbitux); panitumumab (Vectibix); everolimus (Afinitor); alemtuzumab (Campath); gemtuzumab (Mylotarg); temsirolimus (Torisel); pazopanib (Votrient); dasatinib (Sprycel); nilotinib (Tasigna); vatalanib (Ptk787; ZK222584); CEP-701; SU5614; MLN518; XL999; VX-322; Azd0530; BMS-354825; SKI-606 CP-690; AG-490; WHI-P154; WHI-P131; AC-220; and AMG888.
 10. The method of claim 1, wherein the one or more tyrosine kinase inhibitors includes sunitinib.
 11. The method of claim 1, wherein the one or more VEGF/VEGFR inhibitors are selected from bevacizumab (Avastin); sorafenib (Nexavar); sunitinib (Sutent); ranibizumab; pegaptanib; vandetinib; E7080; Zd6474; PKC-412; Vatalanib (Ptk787 or ZK222584); and motesanib diphosphate.
 12. The method of claim 1, wherein the one or more VEGF/VEGFR inhibitors includes sunitinib.
 13. The method of claim 1, wherein the EZH2 inhibitor and the one or more tyrosine kinase inhibitors are administered simultaneously or sequentially.
 14. The method of claim 1, wherein the EZH2 inhibitor is administered prior to administration of the one or more tyrosine kinase inhibitors.
 15. The method of claim 1, wherein the EZH2 inhibitor and the one or more VEGF/VEGFR inhibitors are administered simultaneously or sequentially.
 16. The method of claim 1, wherein the EZH2 inhibitor is administered prior to administration of the one or more VEGF/VEGFR inhibitors.
 17. The method of claim 1, wherein the cancer is renal cell carcinoma. 